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Building and Sustaining a Community Resource for Best Practices in Scientific Software: The Story of BSSw.io

The development of scientific software—a cornerstone of long-term collaboration and scientific progress—parallels the development of other types of software but still poses distinct challenges, especially in high-performance computing. Although web searches yield numerous resources on software engineering, there is still a scarcity specifically for scientific software development. Here, this article introduces the Better Scientific Software site (https://bssw.io), a platform that hosts a community of researchers, developers, and practitioners who share their experiences and insights on scientific software development. Since 2017, this collaborative hub has gained traction within the scientific computing community, attracting a growing number of readers and contributors eager to share ideas and elevate their software development practices. In sharing the BSSw.io site’s story, we hope to encourage further growth of the BSSw.io community through both readership and contributors, with a long-term goal of fostering culture change by increasing emphasis on best practices in scientific software.

97 MATHEMATICS AND COMPUTING↗

Integrating Machine-learning-assisted Computer Vision with RICH System

Developments in artificial intelligence have vastly expanded the capabilities of robots. Currently, the Spallation Neutron Source (SNS) beamlines at Oak Ridge National Lab (ORNL) have robotic sample loaders to increase the efficiency of running experiments. However, they require retraining if anything about the situation changes, e.g., where the samples are, and cannot notice if errors occur. So, the viability of using computer vision and machine learning to enhance these sample loaders’ functionality was investigated. In this project, the RICH system with a Dobot CR3 6-axis robot present at the VULCAN beamline assisted by an Intel Realsense D435i camera, a unique camera that enables convenient translation of 2D pixel coordinates to 3D world points, was programmed to load ceramic crucibles into a thermogravimetric analyzer (TGA) furnace. An algorithm was constructed in Python with three major phases planned: (1) obtaining a sample, (2) moving it to the target location, and then (3) bringing the sample back to its original location once the experiment finished. In the first phase, the algorithm would dynamically detect sample locations using ArUco markers to recognize the samples’ general location and a custom-trained yolov5 object detection model to locate the crucibles’ centers. Afterward, the robot would be directed to pick up samples based on the crucibles’ calculated positions. In the second phase, the robot would move the sample to a secondary point, reorient its grip, and place the sample at the target location. In the final phase, the robot would determine whether the sample was intact and would bring it back to its original place if it was or raise an alarm. Using this algorithm, the robot was able to pick up different types of crucibles at varying positions. These results indicate that integrating machine-learning-assisted computer vision with robotic sample loaders can result in effective autonomous detection of samples.

97 MATHEMATICS AND COMPUTING↗

Intelligent experiments through real-time AI: Fast Data Processing and Autonomous Detector Control for sPHENIX and future EIC detectors (Phase-I)

With an ever increasing demand for high precision data from modern detectors for discovery science and precision measurements, all major high energy nuclear and particle experiments, current and future, are facing the challenge on how to deal with the large volume of raw data generated from sophisticated state-of-the-art detectors in high rate collisions. These goals need to be balanced with available hardware and cost limits on DAQ (Data AcQuisition system) bandwidth and offline computing resources to capture, store and process the signal events. Two prototypical examples are the upcoming sPHENIX experiment, the DOE next generation heavy ion physics experiment at the Relativistic Heavy Ion Collider at BNL, and the future EIC experiments that are planned to be online circa 2030.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Anisotropy and isotope effect in superconducting solid hydrogen

Elucidating the phase diagram of solid hydrogen is a key objective in condensed matter physics. Several decades ago, it was proposed that at low temperatures and high pressures, solid hydrogen would be a metal with a high superconducting transition temperature. This transition to a metallic state can happen through the closing of the energy gap in the molecular solid or through a transition to an atomic solid. Recent experiments have managed to reach pressures in the range of 400–500 GPa, providing valuable insights. There is strong evidence suggesting that metallization via either of these mechanisms occurs within this pressure range. Computational and experimental studies have identified multiple promising crystal phases, but the limited accuracy of calculations and the limited capabilities of experiments prevent us from determining unequivocally the observed phase or phases. Therefore, it is crucial to investigate the superconducting properties of all the candidate phases. Recently, we reported the superconducting properties of the C2/c-24, Cmca-12, Cmca-4 and I41/amd-2 phases, including anharmonic effects. Here, we report the effects of anisotropy on superconducting properties using Eliashberg theory. Then, we investigate the superconducting properties of deuterium and estimate the size of the isotope effect for each phase. We find that the isotope effect on superconductivity is diminished by anharmonicity in the C2/c-24 and Cmca-12 phases and enlarged in the Cmca-4 and I41/amd-2 phases. Our anharmonic calculations of the C2/c-24 phase of deuterium agree closely with the most recent experiment by Loubeyre et al (2022 Phys. Rev. Lett.29 035501), indicating that the C2/c-24 phase remains the leading candidate in this pressure range, and has a strong anharmonic character. These characteristics can serve to distinguish among crystal phases in experiment. Furthermore, expanding our understanding of superconductivity in pure hydrogen holds significance in the study of high-T c hydrides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-pressure phase diagram of beryllium from ab initio free-energy calculations

In this report we use first-principles molecular dynamics simulations coupled with the thermodynamic integration method to study the hexagonal close-packed (hcp) to body-centered cubic (bcc) transition and melting of beryllium up to a pressure of 1600 GPa. We derive the melting line by equating solid and liquid Gibbs free energies and represent it by a Simon-Glatzel fit T m = 1564 K [1 + P/(15.6032 GPa)] 0.383 , which is in good agreement with previous two-phase simulations <6000 K. We also derive the hcp-bcc solid-solid phase boundary and show that the quasiharmonic approximation underestimates the stability of the hcp structure, predicting lower transition pressures between hcp and bcc phases. Our results are consistent with the stability regime predicted by the phonon quasiparticle method. We also predict that the hcp-bcc-liquid triple point is located at 164.7 GPa and 4314 K. In addition, we compute the shock Hugoniot curve and show that it is in good agreement with experiments, intersecting our derived melting curve at ~235 GPa and 4900 K. Finally, we make predictions for future ramp compression experiments. Starting with an isentropic compression of the liquid, we predict the path to intersect the melting line at low pressure and temperature, then to continue along the melting line over a large temperature interval of 7000 K as the sample remains in the mixed solid-liquid state before it enters the solid phase.

36 MATERIALS SCIENCE↗

A method for characterization of multiple dynamic constitutive parameters of FRCs

We propose a method to measure multiple dynamic material constitutive parameters of unidirectional fiber reinforced composites (FRCs) in a single experiment. Dynamic short-beam shear (DSBS) experiments were performed on a modified Kolsky compression bar, with integration of high-speed imaging and digital image correlation (DIC). The unidirectional FRCs investigated were S-2 glass fiber reinforced matrix of TGDDM-Jeffamine® D230 with monoamine functionalized partially reacted substructures (mPRS) and commercially available SC-15. Analytical solutions of normal and shear strains of a composite beam were derived based on Timoshenko beam theory, assuming material to be transversely isotropic and have different moduli in tension and compression in each principle material orientation. Tensile and compressive moduli were inversely computed through monitoring normal strain slope when specimen was constantly loaded at a speed of ~7.3 m/s within a small deflection. Non-linear shear stress-strain behavior of the composite was described via Ramberg–Osgood equation. Finite element (FE) analysis was conducted in ABAQUS, simultaneously defining via user subroutine UMAT the transverse isotropy of material, bi-modulus constitutive model, and non-linear shear stress-strain relation. The method proposed in this work was validated by comparing strain distributions computed by FE model and DIC measurements. Comparing with traditional dynamic tensile, compressive, and shear experiments on FRCs, this method significantly simplifies the specimen preparation and design of complicated gripping fixtures for multiple experiments. Here, systematic errors resulting from variations of specimen geometry and dimension, loading direction, and instrumentation are reduced, thereby providing compatible data for numerical studies on impact behavior of composites.

36 MATERIALS SCIENCE↗

Intrusive Uncertainty Quantification and Optimal Experiment Design in the Open-Source Pyomo Ecosystem

This contribution describes ParmEst and Pyomo.DoE, two pillars of the open-source Python-based Pyomo ecosystem for computational optimization with (partial differential) algebraic equation mathematical models. Specifically, ParmEst facilitates intrusive frequentist parameter estimation (PE) and uncertainty quantification (UQ) through built-in features, such as covariance matrix estimation, bootstrapping, and likelihood ratio tests. Complementary, Pyomo.DoE enables optimal experiment design by maximizing various metrics of the Fisher information matrix, such as A-optimality (trace), D-optimality (determinant), E-optimality (minimum eigenvalue), and ME-optimality (condition number). ParmEst and Pyomo.DoE can solve high-dimensional optimization problems by leveraging the model structure and exact derivative information. Finally, we will discuss future opportunities to integrate PE and UQ capabilities with optimization under uncertainty, including robust optimization with non-convex models via PyROS.

97 MATHEMATICS AND COMPUTING↗

Structure-preserving neural networks for the regularized entropy-based closure of a linear, kinetic, radiative transport equation

The main challenge of large-scale numerical simulation of radiation transport is the high memory and computation time requirements of discretization methods for kinetic equations. In this work, we derive and investigate a neural network-based approximation to the entropy-based closure method to accurately compute the solution of the multi-dimensional moment system with a low memory footprint and competitive computational time. We extend methods developed for the standard entropy-based closure to the regularized entropy-based closures. The main idea is to interpret structure-preserving neural network approximations of the regularized entropy-based closure as a two-stage approximation to the original entropy-based closure. We conduct a numerical analysis of this approximation and investigate optimal parameter choices. Our numerical experiments demonstrate that the method has a much lower memory footprint than traditional methods with competitive computation times and simulation accuracy. The code and all trained networks are provided on GitHub.

entropy closure↗

Very small-scale, segregating-fluidized-bed experiments: A dataset for CFD-DEM validation and uncertainty quantification

IWe report fluidization experiments were conducted on a small scale and with a rapid response (short duration) to enable corresponding simulations at low-computational cost. Rise times are reported for four or fewer polyethylene particles (intruders) in an air-fluidized bed of ~5000 group D glass beads. Experimental inputs were completely characterized—particle properties, system dimensions and operating conditions—which is necessary for validating computational fluid mechanics (CFD)-discrete element method (DEM) including a comprehensive uncertainty quantification (UQ) analysis. Input uncertainties are reported as bounds or cumulative distribution functions of measured values. The staggering number of simulations required to complete a UQ analysis (~O[10 4 ] simulations corresponding to ~5 uncertain inputs) motivates this study. These segregating-bed experiments are designed to permit analogous CFD-DEM simulations to complete in less than a day on a single (~2.5 GHz) computational processor unit (CPU). Segregation times are reported for several operating conditions, intruder sizes, and initial configurations, providing a rich dataset for numerical model testing, validation and UQ.

42 ENGINEERING↗

Measurement of the anomalous precession frequency in the Muon $g-2$ experiment at Fermilab

The muon anomalous magnetic moment, $a_\mu=\frac{g-2}{2}$, is a low energy observable that can be both measured and computed with high precision, therefore it can provide an important test of the Standard Model and it is a sensitive probe for new physics. In particular, any discrepancy between the experimental value and the theoretical prediction can be due to Beyond Standard Model physics contribution. The E989 Muon $g-2$ Experiment at Fermilab aims to measure $a_\mu$ with a precision of 140 parts per billion, four time more precisely than the previous experiment at Brookhaven National Laboratory (BNL). E989 seeks to either resolve or confirm the observed discrepancy of $3.7\sigma$ between the Standard Model value and the experimental one. The $a_\mu$ measurement requires a precise determination of both the muon spin anomalous precession frequency and the average magnetic field seen by the muons as they circulate in a storage ring. The anomalous precession frequency measurement is b ased on the time distribution of high-energy decay positrons observed by 24 electromagnetic calorimeters placed around the inner circumference of the ring, while the magnetic field is constantly monitored by NMR probes. Last spring, E989 has published a new measurement of $a_\mu$ from the 2018 data-taking campaign, confirming the previous BNL value with comparable precision, bringing the discrepancy with the theoretical value to $4.2\sigma$. The candidate worked on the measurement of the anomalous precession frequency and on the estimate of the related systematic uncertainties of the 2018 data, giving an important contribution to the data analysis. The result presented in chapters 4 and 5 of this dissertation was included, among three other analyses, to determine the estimate of the anomalous magnetic moment by the Muon g-2 experiment. This work will present the anomalous precession frequency analysis technique and its result, the related systematics and finally the latest $a_\mu$ result.

Sorbara, Matteo↗

Numerical Investigation of the Spark Discharge Process in a Crossflow

The present study numerically investigates the spark discharge process under crossflow conditions using a thermal equilibrium plasma solver that fully couples the electromagnetic physics and fluid dynamics in a computational framework. Numerical results are validated by the comparison with experimental data. Here, the spark discharge experiment is performed in a constant volume vessel using an inductive coil ignition system for automotive applications, and the evolution of the spark channel is measured using high-speed imaging. The crossflow in the gap between the spark-plug electrodes is generated by a rotating fan with two different fan speeds, and the flow velocity across the gap is characterized by particle image velocimetry (PIV) measurement. A computational fluid dynamics (CFD) solver is employed to simulate the crossflow and provide the flow field variables (velocity, pressure, temperature) to the plasma solver. The crossflow velocity predicted in the flow simulation agrees well with the PIV data in that the non-uniform velocity profiles at monitoring points are reproduced by the CFD code. With the crossflow initialization in the plasma solver, the simulated spark discharge process from the breakdown to spark discharge matches the experimental data, including the voltage and circuit waveforms and the high-speed images of the spark channel evolution. The stretch of spark channel captured by plasma simulations agrees with the measured data. The plasma simulation reveals that the mean temperature of the spark channel is maintained at 5000 K during the discharge phase, and the temperature varies along the spark channel so that the highest value is obtained at the spark root on the center electrode. Overall, the results presented in this paper are meant to provide valuable information about the properties of the plasma generated by the spark discharge.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Determining Multi-Component Phase Diagrams with Desired Characteristics Using Active Learning

Herein, we demonstrate how to predict and experimentally validate phase diagrams for multi-component systems from a high-dimensional virtual space of all possible phase diagrams involving several elements based on small existing experimental data. The experimental data for bulk phases for known systems represents a sampling from this space, and screening the space allows multi-component phase diagrams with given design criteria to be built. This approach uses machine learning methods to predict phase diagrams and Bayesian experimental design to minimize experiments for refinement and validation, all within an active learning loop. The approach is proven by predicting and synthesizing the ferroelectric ceramic system (1-ω)(Ba 0.61 Ca 0.28 Sr 0.11 TiO 3 )-ω(BaTi 0.888 Zr 0.0616 Sn 0.0028 Hf 0.0476 O 3 ) with a relatively high transition temperature and triple point, as well as the NiTi-based pseudo-binary phase diagram (1-ω)(Ti 0.309 Ni 0.485 Hf 0.20 Zr 0.006 )-ω(Ti 0.309 Ni 0.485 Hf 0.07 Zr 0.068 Nb 0.068 ) designed for high transition temperature (ω ≤ 1). Each phase diagram is validated and optimized through only three new experiments. The complexity of these compounds is beyond the reach of today’s computational methods.

36 MATERIALS SCIENCE↗

Design and evaluation of alphabetic and numeric input methods for virtual reality

In today’s virtual reality (VR), users have various ways to influence their VR experience, including alphanumeric input. While typing characters and numbers is straightforward on desktop computers, it presents challenges and opportunities in head-mounted display VR due to specific interaction methods and a lack of real-world visual stimuli. Addressing these open questions, our work implements and evaluates ten approaches to alphabetic and numeric inputs in VR. Here, we describe the design motivation behind these input methods and evaluate them in a user study with 40 participants divided into groups for alphabetic and numeric keyboards. This comparison investigates each method’s performance and user interactions. Our findings suggest that different input methods significantly impact words per minute and error rates, and that certain keyboard designs may receive better subjective evaluations despite poorer objective performance.

97 MATHEMATICS AND COMPUTING↗

Origin of the background absorption in carbon nanotubes: Phonon-assisted excitonic continuum

Excitonic effects in 1D semiconductors can be qualitatively different from those in higher dimensions. In particular, the Sommerfeld factor, the ratio of the above-band-edge excitonic continuum absorption to free electron-hole pair generation, has been shown to be less than 1 (suppressed) in 1D systems while it is larger than 1 (enhanced) in 2D and 3D systems. Strong continuum suppression indeed exists in semiconducting single-wall carbon nanotubes, a prototypical 1D semiconductor. However, absorption spectra for carbon nanotubes are typically fit with a combination of Lorentzians and a polynomial background baseline with little physical meaning. We performed absorption measurements in aligned single-chirality (6,5) carbon nanotube films. The obtained spectra were fit with our theoretical model obtained by solving the Boltzmann scattering equation involving fifty-nine different types of transitions among three different types of quasiparticles. Specifically, we took into account microscopic interactions between photons, phonons, and excitons, including their dispersions, which unambiguously demonstrated that the background absorption is due to phonon-assisted transitions from the semiconductor vacuum to finite-momentum continuum states of excitons. The excellent agreement we obtained between experiment and theory suggests that our numerical technique can be seamlessly extended to compute strongly out-of-equilibrium many-body dynamics and time-resolved spectra in low-dimensional materials.

36 MATERIALS SCIENCE↗

Influence of crystal structure on constitutive anisotropy of silica sand at particle-scale

In spite of recent advanced geotechnical research regarding the influence of particle-scale morphology and fabric on the constitutive behavior of silica sands, there is still no published literature that investigated the influence of crystal structure of sand particles on their constitutive behavior. The main constituent of silica sand particles is quartz mineral, which has a trigonal crystal system and hexagonal lattice. This paper investigates the influence of quartz crystal structure on the constitutive response of silica sand particles using 3D X-ray diffraction (3DXRD), synchrotron micro-computed tomography (SMT), and 3D finite element (FE) analysis. Here, unconfined uniaxial compression experiments on single particles of synthetic silica cubes exposed the notion of constitutive anisotropy caused by the crystal structure of quartz. Since the silica cubes have simple regular geometry (1 mm) 3 , they were loaded in different directions with respect to their crystal local planes. The crystal structure was also identified for a natural silica sand specimen composed of 2705 particles and loaded in confined uniaxial compression. Physical limitations of the experimental measurements made a strong case for the use of 3D FE analysis to study how the change in crystal local orientation of individual sand particles can fundamentally produce anisotropy in the constitutive response of natural sand specimens. The 3D FE analysis was validated to accurately model the crystal-based constitutive anisotropy in silica particles using the results of the silica cube experiments. The analysis was then executed on 3D FE meshes that closely matched the physical shape and fabric of the 2705 particles in the natural sand specimen. Both the experiments and 3D FE analysis showed that the crystal structure of quartz essentially causes a directional anisotropy in the constitutive behavior of silica particles.

58 GEOSCIENCES↗

Magnetosynthesis Effect on the Structure and Ground State of Cu 2+ -Based Antiferromagnets

Synthetic variables can have an outsized influence on the crystal structure and magnetic properties of a material, particularly those of quantum materials. In this work, we investigate the impact of synthesis under a magnetic field (magnetosynthesis) on the crystal structure and magnetic properties of several Cu 2+ (S = 1/2)-based materials with antiferromagnetic interactions and varying levels of magnetic frustration, from simple antiferromagnets to a quantum spin liquid. Here, we develop methods to apply small (0.09–0.37 T) magnetic fields during low-temperature hydrothermal, evaporative, and rehydration syntheses of the simple antiferromagnet CuCl 2 ·2H 2 O, the canted antiferromagnet (Cu,Zn) 3 Cl 4 (OH) 2 ·2H 2 O, the frustrated and canted antiferromagnet atacamite Cu 2 (OH) 3 Cl, and the highly frustrated quantum spin liquid herbertsmithite Cu 3 Zn(OH) 6 Cl 2 . We report the first single-crystal X-ray structural determination of the Cu 3 Cl 4 (OH) 2 ·2H 2 O structure type and probe the stability of this phase both experimentally and computationally. Atacamite Cu 2 (OH) 3 Cl synthesized under a 0.19 T field experiences a 0.15 K (∼3%) decrease in its Néel transition temperature. This result suggests that magnetosynthesis with small applied fields may have a very subtle influence upon the magnetic properties of moderately magnetically frustrated 3 d materials.

36 MATERIALS SCIENCE↗

Constructing the Mechanism of Dinoflagellate Luciferin Bioluminescence Using Computation

Dinoflagellate luciferin bioluminescence is unique since it does not rely on decarboxylation but is poorly understood compared to that of firefly, bacteria, and coelenterata luciferins. Here, in this work, we computationally investigate possible protonation states, stereoisomers, a chemical mechanism, and the dynamics of the bioluminescence intermediate that is responsible for chemiexcitation. Using semiempirical dynamics, time-dependent density functional theory static calculations, and a correlation diagram, we find that the intermediate’s functional group that is likely responsible for chemiexcitation is a 4-member ring, a dioxetanol, that undergoes [2π + 2π] cycloreversion and the biolumiphore is the cleaved structure. The simulated emission spectra and luciferase-dependent absorbance spectra agree with the experimental data, giving support to our proposed mechanism and biolumiphore. We also compute circular dichroism spectra of the intermediate’s four stereoisomers to guide future experiments in differentiating them.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-Fidelity Bayesian Optimization with Gaussian Processes for Double Shell Inertial Confinement Fusion Target Design

Reliable, secure access to energy is a major focus for national security efforts. One potential route to such energy is through fusion reactions in inertial confinement fusion (ICF) experiments. Such experiments are carried out at facilities such as the National Ignition Facility (NIF) in Livermore, California, where high powered lasers are used to compress a DT fuel-containing target to the necessary high temperature, high pressure conditions. These experiments are limited in number, which creates a heavy dependence on high fidelity predictive physics simulations and analysis performed “pre shot,” or before the experiment occurs. Many of these simulations in higher dimensions (2D and 3D) are computationally expensive, so finding optimal simulation-based designs presents its own challenges. In this work, we present our multi-fidelity Bayesian optimization with Gaussian processes (GPs) for ICF double shell targets, where a 1D surrogate model is used to help find a 2D surrogate model, enabling us to find optimal targets in the higher fidelity (2D), while saving computational cost.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗