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The case for free and open source software in research and scholarship

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Here, our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today.

97 MATHEMATICS AND COMPUTING↗

Fundamental Optical Functions and Fine-Structure Parameters of Strontium–Selenide Crystal Transition Bands in the 0–40 eV Range

The spectral complex of fundamental optical functions of strontium-selenide (SrSe) crystal in the range 0–40 eV was determined. Spectra of the imaginary parts of three functions [transverse dielectric permittivity ε{sub 2}(E) and longitudinal volume –Im ε{sup –1} and surface –Im (1 + ε){sup –1} characteristic electron energy losses] of SrSe crystal were deconvoluted into 36 elementary bands. Energies of maxima E{sub i}, half-widths H{sub i}, amplitudes I{sub i}, areas S{sub i}, and oscillator strengths f{sub i} were determined for every band of the three spectra. The main spectral features of the optical functions and 36 elementary bands of SrSe in the range 3–35 eV due to excitons and transverse and longitudinal interband transitions were established. The calculations were based on experimental reflectance spectra and used the Kramers–Kronig integral relations, a modified combined Argand diagram method, and a number of computer programs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Benchmark problems in aerosol evolution: Comparison of some exact and DSMC results

Aerosols are generated in many normal or accident situations associated with the nuclear enterprise. For a good understanding and modeling of the nuclear source term, for example, good experimental data and computational programs relating to aerosol evolution are needed. In the past several years there has been an effort to explore use of the Direct Simulation Monte Carlo (DSMC) approach for such estimations to improve fidelity of computations to the actual physics and chemistry of the accidents. An integral part of these efforts has been verification and validation of the DSMC technique against other available results wherever possible. Herein this paper explores verification of DSMC against one existing and two new benchmark problems covering condensation, coagulation, deposition and two-component aerosols. The simulations compare well with the exact results, providing further confidence in the use of DSMC.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Simulation of Motion of H{sub 2} and D{sub 2} Molecules in Sextupole Magnets

We simulate the motion of hydrogen and deuterium molecules in the magnetic system of a setup intended for obtaining nuclear-spin-polarized molecules. Spatial separation of molecules with different magnetic moment projections by the spin filtration method in a nonuniform magnetic field is performed using superconducting sextupole magnets. Calculations are carried out for a magnetic field induction of 3.7 T at the poles and a nozzle temperature of 7 K. Simulation show that the ratio of polarized flux of hydrogen molecules to the detector to the total flux from the source nozzle is 2.3 × 10{sup –6}, nuclear polarization being close to 100%. Calculations performed for deuterium reveal that this ratio is 7 times smaller due to the smallness of the magnetic moment relative to hydrogen molecules. Trajectories of molecules in the magnetic system and their spatial distribution are represented graphically. Mathematical aspects of the algorithm of the computer program developed for this purpose are considered.

74 ATOMIC AND MOLECULAR PHYSICS↗

Spinteract: a program to refine magnetic interactions to diffuse scattering data

Magnetic diffuse scattering—the broad magnetic scattering features observed in neutron-diffraction data above a material's magnetic ordering temperature—provides a rich source of information about the material's magnetic Hamiltonian. However, this information has often remained under-utilised due to a lack of available computer software that can fit values of magnetic interaction parameters to such data. Here, an open-source computer program, Spinteract, is presented, which enables straightforward refinement of magnetic interaction parameters to powder and single-crystal magnetic diffuse scattering data. Here, the theory and implementation of this approach are summarised. Examples are presented of refinements to published experimental diffuse-scattering data sets for the canonical antiferromagnet MnO and the highly-frustrated classical spin liquid Gd 3 Ga 5 O 12 . Guidelines for data collection and refinement are outlined, and possible developments of the approach are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SonicPy: a suite of programs for ultrasound pulse-echo data acquisition and analysis

Sound speed and elastic constants measurements in solids and liquids are commonly performed using the ultrasound pulse-echo technique. Recent advances have expanded the use of this technique at numerous high pressure synchrotron beamlines and offline laboratories. However, the increased experimental throughput has revealed many limitations in existing software for handling the rapid measurement and the subsequent data-reduction. Here, we report the development of a collection of computer programs for sound speed measurements using the ultrasound pulse-echo technique, compatible with stepped multi-frequency, as well as broadband-pulse, couplant-corrected methods. The programs provide a highly interactive graphical interface, enable efficient measurement, exploration and near real-time analysis of the ultrasound data, and contain features useful for working with samples under high pressure and/or high temperature. The included analysis programs can alleviate the time required for data reduction from hours to less than a minute, allowing users to make timely and informed decisions regarding the appropriate experimental parameters.

97 MATHEMATICS AND COMPUTING↗

Global Benefits: the LBNF/DUNE Project

LBNF/DUNE is an international mega-science project hosted by the Department of Energy’s Fermilab. http://www.fnal.gov/dune It will send a beam of tiny particles called neutrinos 1,300 kilometers straight through the earth from Fermilab to the Sanford Underground Research Facility. It will help solve some of the deepest mysteries of the universe and boost innovation while training young people around the world in science, engineering and computing. Scientists and engineers at universities and laboratories are working hand-in-hand with companies to design electronics, build hardware and develop computer programs for the project. LBNF and DUNE will create jobs as well as demand for materials, products and services. Students in dozens of countries around the world will start their careers in science and engineering with this project, and then transfer their knowledge into industry, medicine, computer science and many other fields.

43 PARTICLE ACCELERATORS↗

Monte Carlo Hauser-Feshbach computer code system to model nuclear reactions: YAHFC

A computer program framework, YAHFC, to model low-energy nuclear reactions is presented. The framework allows for reactions with incident particles ranging from protons/neutrons to alphas and is designed to address reactions that ultimately lead to the formation of compound nuclear systems that then decay statistically as outlined in concepts of Hauser and Feshbach. Additionally, instead of a reaction, it is also possible to model the decay of a nuclear system with an initial excitation and population. The code models nuclear decays with a Monte Carlo process that tracks the decay of each state. This allows for an exact representation of the spectra for all emitted particles in each of the final exit channels and the possibility of generating reaction data for simulation purposes. The program is interfaced with the optical model code system FRESCOX to calculate transmission coefficients as well as the effects of coupled channels and other direct excitations via the distorted wave Born approximation (DWBA). Modules are included to account for nuclear processes such as width corrections, pre-equilibrium emission, and fission. The program is controlled by a series of input commands and while a set of input parameters exists for each projectile and target, the input commands allow for complete control over each input parameter. Extensive data files are produced and a program is provided that converts YAHFC data files into nuclear data library entries in the generalized nuclear data structure (GNDS).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The CanBikeCO Mini Pilot: Procedure and Preliminary Results

In fall 2020, the Colorado Energy Office, as part of the State of Colorado's "Can Do Colorado" initiative, initiated a project aimed at encouraging energy-efficient transportation during the COVID-19 pandemic. The initial mini-pilot provided e-bikes to 13 low-income households under an individual ownership model. This report assesses the impact of providing this additional mobility option on the travel behavior of participants. It also outlines the lessons learned from deploying a continuous monitoring platform to track the travel behavior. These lessons will influence the evaluation component for the full pilot, which will cover multiple geographic regions, start in summer 2021, and run for 2 years. The continuous data collection was enabled by a customized version of the open-source e-mission platform, called CanBikeCO, configured with a behavioral gamification feature. The Colorado Energy Office used this system to collect a unique data set consisting of 3 months of partially automated travel diaries, combining sensed and surveyed data and linked with demographic information, from 12 participants. The data collection process worked well overall: users generally liked the app, appreciated the game, and did not complain about battery life. The long tracking period introduced behavioral challenges in user engagement, which we plan to address using repeated patterns and automated status checks for the full pilot. The analysis results, based on the subset of trips with user-reported labels (68%), indicate that the e-bike was the dominant commute mode share (31%), in sharp contrast to the census bicycle commute mode share (<1%). E-bike trips primarily replaced single-occupancy vehicle (SOV) trips (28%), followed closely by walking (24%) and regular bike (20%). The non-motorized mode replacement corresponds to lower travel time and increased productivity enabled by the program. The emissions impact analysis of the program, computed using trip-level energy intensity factors, indicates savings of 1,367 lbs. of CO2. Although the results are strongly positive, the narrow demographic profile of study participants, their limited mobility alternatives, and nonuniform labeling indicate caution in broader interpretation. These preliminary results do suggest that such programs, supported by real-time education and support from program managers, can simultaneously meet equity and sustainability goals. The planned full pilot, addressing the data collection challenges and broadening the geographic scope, will provide additional insights into the generality of this approach.

ADVANCED PROPULSION SYSTEMS↗

The CanBikeCO Mini Pilot: Preliminary Results and Lessons Learned

In fall 2020, the Colorado Energy Office, as part of the State of Colorado’s “Can Do Colorado” initiative, initiated a project aimed at encouraging energy-efficient transportation during the COVID-19 pandemic. The initial mini-pilot provided e-bikes to 13 low-income households under an individual ownership model. This report assesses the impact of providing this additional mobility option on the travel behavior of participants. It also outlines the lessons learned from deploying a continuous monitoring platform to track the travel behavior. These lessons will influence the evaluation component for the full pilot, which will cover multiple geographic regions, starting in summer 2021, and run for 2 years. The continuous data collection was enabled by a customized version of the open-source e-mission platform, called CanBikeCO, configured with a behavioral gamification feature. The Colorado Energy Office used this system to collect a unique data set consisting of 3 months of partially automated travel diaries, combining sensed and surveyed data and linked with demographic information, from 12 participants. The data collection process worked well overall: users generally liked the app, appreciated the game, and did not complain about battery life. The long tracking period introduced behavioral challenges in user engagement, which we plan to address using repeated patterns and automated status checks for the full pilot. The analysis results, based on the subset of trips with user-reported labels (68%), indicate that the e-bike was the dominant commute mode share (31%), in sharp contrast to the census bicycle commute mode share (<1%). E-bike trips primarily replaced single-occupancy vehicle (SOV) trips (28%), followed closely by walking (24%) and regular bike (20%). The nonmotorized mode replacement corresponds to lower travel time and increased productivity enabled by the program. The emissions impact analysis of the program, computed using trip-level energy intensity factors, indicates savings of 1,367 lbs. of CO 2 . Although the results are strongly positive, the narrow demographic profile of study participants, their limited mobility alternatives, and nonuniform labeling indicate caution in broader interpretation. These preliminary results do suggest that such programs, supported by real-time education and support from program managers, can simultaneously meet equity and sustainability goals. The planned full pilot, addressing the data collection challenges and broadening the geographic scope, will provide additional insights into the generality of this approach.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Batched Sparse Linear Algebra Phase 2 (Final Report)

The purpose of the work was to help LLNL develop a broadly applicable set of capabilities that focus on batched sparse linear functionality and its software implementation. The enablement occurred in a broader scope of the Exascale Computing Program (ECP) with an eye on the xSDK collection of applications and libraries. These served as the main dissemination targets and in the end benefitted from this project’s outcomes.

97 MATHEMATICS AND COMPUTING↗

Batched Sparse Linear Algebra Phase 2

The purpose of the work was to help LLNL develop a broadly applicable set of capabilities that focus on batched sparse linear functionality and its software implementation. The enablement occurred in a broader scope of the Exascale Computing Program (ECP) with an eye on the xSDK collection of applications and libraries. These served as the main dissemination targets and in the end benefitted from this project’s outcomes.

97 MATHEMATICS AND COMPUTING↗

Investing in STEM Benefits Community, Company, and Industry - 20243

Like many organizations and groups, the Department of Energy Environmental Management program and the nuclear industry are facing an aging employee population and record numbers of employee retirements. This 'silver tsunami' of retirees means the industry as a whole is recruiting graduates at a fast pace. So, how do we ensure the nuclear industry has a robust pipeline of graduates with the necessary background? Fluor Idaho's investment in science, technology, engineering, and mathematics (STEM) education programs helps promote the next generation of technical professionals, benefiting both the company and the industry. Through community outreach initiatives and student mentoring programs, Fluor Idaho promotes kids' interest in STEM. The programs are designed to spark STEM interest in grade school and then foster and grow that interest through high school and higher education. After igniting student excitement about STEM topics in school, Fluor Idaho focuses on providing work-specific opportunities including mentoring and intern programs. These programs give students a better look at real-world job opportunities while still stimulating their interest in STEM. These programs ultimately provide career opportunities for the students and a pipeline of workers. Fluor Idaho's strategy for its summer interns has been to place students in a wide variety of projects - from the commissioning of a first-of-a-kind nuclear processing facility, to operating nuclear waste management facilities, to developing computer programs and applications - and give them responsibilities that make them feel like valued contributors. This approach has created a positive and rewarding summer-intern program experience for the students. Fluor Idaho's investment in its future today is reducing the knowledge gap - or cliff - that many contractors in the nuclear industry are facing. It's a worthwhile investment that is readily visible within its many cleanup projects. The next generation of technical professionals is making an impact now - benefiting both the company and the nuclear industry. This paper will review Fluor Idaho's programs, including STEM community outreach and education and mentoring programs. It will also present statistics about the reach of those programs and their successes. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Local Petrovskii lacunas close to parabolic singular points of the wavefronts of strictly hyperbolic partial differential equations

We enumerate the local Petrovskii lacunas (that is, the domains of local regularity of the principal fundamental solutions of strictly hyperbolic PDEs with constant coefficients in R{sup N}) close to parabolic singular points of their wavefronts (that is, at the points of types P{sub 8}{sup 1}, P{sub 8}{sup 2}, ±X{sub 9}, X{sub 9}{sup 1}, X{sub 9}{sup 2}, J{sub 10}{sup 1} and J{sub 10}{sup 3}). These points form the next most difficult family of classes in the natural classification of singular points after the so-called simple singularities A{sub k}, D{sub k}, E{sub 6}, E{sub 7} and E{sub 8}, which have been investigated previously. Also we present a computer program which counts the topologically distinct morsifications of critical points of smooth functions, and hence also the local components of the complement of a generic wavefront at its singular points. Bibliography: 22 titles. (paper)

97 MATHEMATICS AND COMPUTING↗

An Unsteady State Gas Transport Model in Matrix Laboratory (MATLAB) for PWR Gas Management

Reactor Coolant System (RCS) hydrogen gas management can be a challenge at Pressurized Water Reactors (PWRs) during shutdown, startup, and steady state operation. Poor hydrogen control can result in higher general corrosion rates for RCS components and increases in critical path time for shutdown or startup. Also, performance indicator penalties may be accrued by entry into Electric Power Research Institute (EPRI) Action Level conditions or by accrual of Chemistry Effectiveness Index (CEI) penalties established by the Institute of Nuclear Power Operations (INPO). Furthermore, poor hydrogen control may increase industrial safety risk due to the creation of an explosive environment. Part of the hydrogen management difficulty arises from the interaction of several phenomena that require complex simulations to fully understand. While hydrogen gas transport models have been developed, the application of these models is limited by the computational intensity required to accurately model the dynamism inherent in plant shutdown or startup. Subsequently, a gas transport model is developed in a suitable computational program to meet these needs and provide input to an optimized RCS hydrogen management strategy for all operational modes. The gas transport model is used to model RCS hydrogen behavior for an example PWR during an End of Cycle (EOC) Forced Outage (FO) startup, a refueling outage (RFO) shutdown, and during nominal steady state operation. The computational software selected is Matrix Laboratory (MATLAB{sup R})

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Generating and Analyzing Program Call Graphs using Ontology

Call graph or caller-callee relationships have been used for various kinds of static program analysis, performance analysis and profiling, and for program safety or security analysis such as detecting anomalies of program execution or code injection attacks. However, different tools generate call graphs in different formats, which prevents efficient reuse of call graph results. In this paper, we present an approach of using ontology and resource description framework (RDF) to create knowledge graphs for specifying call graphs to facilitate the construction of full-fledged and complex call graphs of computer programs, realizing more interoperable and scalable program analyses than conventional approaches. We create a formal ontology-based specification of call graph information to capture concepts and properties of both static and dynamic call graphs so different tools can collaboratively contribute to more comprehensive analysis results. Our experiments show that ontology enables merging of call graphs generated from different tools and flexible queries using a standard query interface. Index Terms—Callgraph, ontology, knowl

Dorta, E.↗