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DOE OSTI2017

Software aspects of the Geant4 validation repository

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientic Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2014

Watts Bar Unit 1 Cycle Zero Power Physics Tests Analysis with VERA-CS

The Consortium for Advanced Simulation of Light Water Reactors (CASL) is developing a collection of methods and software products known as VERA, the Virtual Environment for Reactor Applications, including a core simulation capability called VERA-CS. A key milestone for this endeavor is to validate VERA against measurements from operating nuclear power reactors. The first step in validation against plant data is to determine the ability of VERA to accurately simulate the initial startup physics tests for Watts Bar Nuclear Power Station, Unit 1 (WBN1) cycle 1. VERA-CS calculations were performed with the Insilico code developed at ORNL using cross section processing from the SCALE system and the transport capabilities within the Denovo transport code using the SPN method. The calculations were performed with ENDF/B-VII.0 cross sections in 252 groups (collapsed to 23 groups for the 3D transport solution). The key results of the comparison of calculations with measurements include initial criticality, control rod worth critical configurations, control rod worth, differential boron worth, and isothermal temperature reactivity coefficient (ITC). The VERA results for these parameters show good agreement with measurements, with the exception of the ITC, which requires additional investigation. Results are also compared to those obtained with Monte Carlo methods and a current industry core simulator.

CASL↗

DOE OSTI2013

Automated x-ray/light field congruence using the LINAC EPID panel

Purpose: X-ray/light field alignment is a test described in many guidelines for the routine quality control of clinical linear accelerators (LINAC). Currently, the gold standard method for measuring alignment is through utilization of radiographic film. However, many modern LINACs are equipped with an electronic portal imaging device (EPID) that may be used to perform this test and thus subsequently reducing overall cost, processing, and analysis time, removing operator dependency and the requirement to sustain the departmental film processor. Methods: This work describes a novel method of utilizing the EPID together with a custom inhouse designed jig and automatic image processing software allowing measurement of the light field size, x-ray field size, and congruence between them. The authors present results of testing the method for aS1000 and aS500 Varian EPID detectors for six LINACs at a range of energies (6, 10, and 15 MV) in comparison with the results obtained from the use of radiographic film. Results: Reproducibility of the software in fully automatic operation under a range of operating conditions for a single image showed a congruence of 0.01 cm with a coefficient of variation of 0. Slight variation in congruence repeatability was noted through semiautomatic processing by four independent operators due to manual marking of positions on the jig. Testing of the methodology using the automatic method shows a high precision of 0.02 mm compared to a maximum of 0.06 mm determined by film processing. Intraindividual examination of operator measurements of congruence was shown to vary as much as 0.75 mm. Similar congruence measurements of 0.02 mm were also determined for a lower resolution EPID (aS500 model), after rescaling of the image to the aS1000 image size. Conclusions: The designed methodology was proven to be time efficient, cost effective, and at least as accurate as using the gold standard radiographic film. Additionally, congruence testing can be easily performed for all four cardinal gantry angles which can be difficult when using radiographic film. Therefore, the authors propose it can be used as an alternative to the radiographic film method allowing decommissioning of the film processor.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Arion

Arion is a library and tool set that enables researchers to holistically define test system models. To define a complex system for testing an algorithm or control requires expertise across multiple domains. Simulating a complex system requires the integration of multiple simulators and test hardware, each with their own specification languages and concepts. This requires extensive set of knowledge and capabilities. Arion was developed to alleviate this challenge. Arion is a library of Java libraries that abstracts the concepts from supported simulators into a cohesive model language that allows someone to build models to their needed level of fidelity and expertise. Arion is also a software tool that translates the users model back into the specification languages of the simulators and test hardware needed for execution.

Fisher, Andy↗

DOE OSTI2016

Arion

Source record↗

DOE OSTI2018

Performance study of atomic tally methods for GPU-accelerated Monte Carlo dose calculation - 25352

Over the past several years, the graphics processing unit (GPU) technology has rapidly gained ground in scientific computing due to its outstanding performance and programmability. GPU implementation of Monte Carlo radiation transport for dose calculations has been reported by many investigators. The majority of these studies adopted single-precision floating point format because of the higher peak floating point operations per second (FLOPS) the GPUs can deliver than double-precision. It has been known that calculation using single-precision is more prone to numerical round-off errors, especially when a single tally data is accumulated 'atomically' and repeatedly by thousands of GPU threads. To mitigate this problem, the least intrusive solution in theory is to replace the single-precision atomic-add tally function with a double-precision version. However, the complexity lies in the fact that some GPUs (Nvidia GPUs prior to the Pascal generation; all current AMD GPUs) do not readily offer such double-precision function at hardware level, and that software emulation is too slow to use if not optimized properly. This paper discusses several atomic-add tally methods with reduced numerical errors used throughout ARCHER development. The original software-based compare-and-swap method (CAS) was shown to be inefficient due to high intra-warp thread contention, whereas the improved software-based warp-aggregated method (WAG) and Kahan summation method (KAS) eliminated the thread contention and performed very well on Kepler and Maxwell GPUs, being more than 13 times faster than CAS in our tests. The hardware-based (HB) double-precision atomic-add feature available on Pascal and Volta GPUs exceeded software emulation and offered the best performance universally, so did WIB, a combination of WAG and HB methods. It was also shown that in a single-precision dose engine, KAS managed to maintain high reliability when the single-precision atomic-add tally underestimated the dose by 25%. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2026

A Scalable Test-Bed for Direct Current Current Transformer Automated Functional Testing and Characterization

This article describes a scalable test-bed for automation of measurements of the direct current current transformers (DCCT). Automation of measurement involves functional measurements, fault event based measurements and data validation. The test-bed is designed to measure up to 20 DCCTs at a time with software based measurement repetition checks and validation of the measurements.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Developing and Managing Data Acquisition Software Using Spack

The Data Acquisition systems of particle physics experiments regularly push the boundaries of high-throughput computing, demanding low-latency collection of data from thousands of devices, collating data into time-sliced events, processing these events and making trigger decisions, and writing the selected data streams to disk. To accomplish these tasks, the DAQ Engineering and Operations department at Fermilab leverages multiple software libraries and builds reusable DAQ frameworks on top. These libraries must be delivered in well-defined bundles and are thoroughly tested for compatibility and functionality before being deployed to live detectors. We have several techniques used to ensure that a consistent set of dependencies can be delivered and re-created at need. We must also support active development of DAQ software components, ideally in an environment as close as possible to that of the detectors. This development often occurs across multiple packages which have to be built in concert and features tested in a consistent and reproducible manner. I will present our scheme for accomplishing these goals using Spack environments, bundle packages, and Github Actions-based CI.

Flumerfelt, Eric [Fermilab]↗

DOE OSTI2013

Evaluation of the Effective Moisture Penetration Depth Model for Estimating Moisture Buffering in Buildings

This study examines the effective moisture penetration depth (EMPD) model, and its suitability for building simulations. The EMPD model is a compromise between the simple, inaccurate effective capacitance approach and the complex, yet accurate, finite-difference approach. Two formulations of the EMPD model were examined, including the model used in the EnergyPlus building simulation software. An error in the EMPD model we uncovered was fixed with the release of EnergyPlus version 7.2, and the EMPD model in earlier versions of EnergyPlus should not be used.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2019

Automatic Analyte-Ion Recognition and Background Removal for Ambient Mass-Spectrometric Data Based on Cross-Correlation

Ambient mass spectrometry is a powerful approach for rapid, high-throughput, and direct sample analysis. Due to the open-air desorption and ionization processes, random fluctuations of ambient conditions can lead to large variances in mass-spectral signals over time. The mass-spectral data also can be further complicated due to multiple analytes present in the sample, background-ion signals stemming from the desorption/ionization source itself, and other laboratory-specific conditions (e.g., ambient laboratory air, nearby hardware). Thus, background removal and analyte-ion recognition can be quite difficult, particularly in non-targeted analyses. Here, we demonstrate the use of a cross-correlation-based approach to exploit chemical information encoded in the time domain to group/categorize mass-spectral peaks from a single analysis dataset. Ions that originate from ambient (or other) background species were readily flagged and removed from spectra; the result was a decrease in mass-spectral complexity by over 70% due to the removal of these background ions. Meanwhile, analyte ions were differentiated and categorized based on their time-domain profiles. With sufficient mass resolving-power and mass-spectral acquisition rate, isolated mass spectra containing ions from the same species in a sample could be extracted, leading to a reduction in mass-spectral complexity by more than 98% in some cases. The cross-correlation approach was tested with different ionization sources as well as reproducible and irreproducible sample introduction. Software built in-house enabled fully automated data processing, which can be performed within a few seconds. Ultimately, this approach provides an additional dimension of analyte separation in ambient mass-spectrometric analyses with information that is already recorded throughout the analysis. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

A non-orthogonal material model of woven composites in the preforming process

Woven composites are considered as a promising material choice for lightweight applications. An improved non-orthogonal material model that can decouple the strong tension and weak shear behaviour of the woven composite under large shear deformation is proposed for simulating the preforming of woven composites. The tension, shear and compression moduli in the model are calibrated using the tension, bias-extension and bending experiments, respectively. The interaction between the composite layers is characterized by a sliding test. The newly developed material model is implemented in the commercial finite element software LS-DYNA® and validated by a double dome study.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA↗

DOE OSTI2021

Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay

Phosphorylation of the histone protein H2AX to form γ-H2AX foci directly represents DNA double-strand break formation. Traditional γ-H2AX detection involves counting individual foci within individual nuclei. The novelty of this work is the application of a time-resolved fluorescence assay using dissociation-enhanced lanthanide fluorescence immunoassay for quantitative measurements of γ-H2AX. For comparison, standard fluorescence detection was employed and analyzed either by bulk fluorescent measurements or by direct foci counting using BioTek Spot Count algorithm and Gen 5 software. Etoposide induced DNA damage in A549 carcinoma cells was compared across all test platforms. Time resolved fluorescence detection of europium as a chelated complex enabled quantitative measurement of γ-H2AX foci with nanomolar resolution. Comparative bulk fluorescent signals achieved only micromolar sensitivity. Lanthanide based immunodetection of γ-H2AX offers superior detection and a user-friendly workflow. These approaches have the potential to improve screening of compounds that either enhance DNA damage or protect against its deleterious effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Comparative analysis of numerical models of pipe handling equipment used in offshore drilling applications

Design of offshore drilling equipment is a task that involves not only analysis of strict machine specifications and safety requirements but also consideration of changeable weather conditions and harsh environment. These challenges call for a multidisciplinary approach and make the design process complex. Various modeling software products are currently available to aid design engineers in their effort to test and redesign equipment before it is manufactured. However, given the number of available modeling tools and methods, the choice of the proper modeling methodology becomes not obvious and – in some cases – troublesome. Therefore, we present a comparative analysis of two popular approaches used in modeling and simulation of mechanical systems: multibody and analytical modeling. A gripper arm of the offshore vertical pipe handling machine is selected as a case study for which both models are created. In contrast to some other works, the current paper shows verification of both systems by benchmarking their simulation results against each other. Such criteria as modeling effort and results accuracy are evaluated to assess which modeling strategy is the most suitable given its eventual application.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Summary Protein property prediction via machine learning with and without labeled data is becoming increasingly powerful, yet methods are disparate and capabilities vary widely over applications. The software presented here, “Artificial Intelligence Driven protein Estimation (AIDE)”, enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods for variants and variable length homologs in a single, reproducible notebook or script by defining a modular, standardized application programming interface (API), i.e. drop-in compatible with scikit-learn transformers and pipelines. Availability and implementation AIDE is an installable, importable python package inheriting from scikit-learn classes and API and is installable on Windows, Mac, and Linux. Many of the wrapped models internal to AIDE will be effectively inaccessible without a GPU, and some assume CUDA. The newest stable, tested version can be found at https://github.com/beckham-lab/aide_predict and a full user guide and API reference can be found at https://beckham-lab.github.io/aide_predict/. Static versions of both at the time of writing can be found on Zenodo.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Applied Metrology for the Assembly of the Nb 3 Sn MQXFA Quadrupole Magnets for the HL-LHC AUP

The US HL-LHC Accelerator Upgrade Project (AUP) is building Nb 3 Sn quadrupole magnets, called MQXFA, with plans to install 16 of them in the HL-LHC Interaction Regions. Variability in coil size must be dealt with at the assembly level, which requires timely and repeatable measurement of each coil. In this paper we will present the methodology used for coil measurements and the geometrical size data for the coils that have been measured thus far. We will also show the coil measurements of 8 coils before and after cold test. In conclusion, the Leica AT960-MR laser tracker with Spatial Analyzer software acquired to achieve these measurements has been used elsewhere in the project to great effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Tools for analysis of optimization models

The software is code for analyzing, debugging, and solving optimization models. The code implements several algorithms and provides convenient APIs to apply these algorithms to optimization models. The algorithms are primarily based on graph theory. They compute well-known partitions of graphs, and use these partitions to provide the user information about their optimization model, including diagnosing certain types of structural modeling errors. Some algorithms may be used as a subroutine to solve an optimization problem, and may call an optimization solver to facilitate this. Well-known linear algebra routines are called to provide further diagnostics. The software contains no data and no models other than toy models used for testing.

Parker, Robert↗

DOE OSTI2025

An HPC benchmark survey and taxonomy for characterization

The field of High-Performance Computing (HPC) is defined by providing computing devices with highest performance for a variety of demanding scientific users. The tight co-design relationship between HPC providers and users propels the field forward, paired with technological improvements, achieving continuously higher performance and resource utilization. A key device for system architects, architecture researchers, and scientific users are benchmarks, allowing for well-defined assessment of hardware, software, and algorithms. Many benchmarks exist in the community, from individual niche benchmarks testing specific features, to large-scale benchmark suites for whole procurements. We survey the available HPC benchmarks, summarizing them in table form with key details and concise categorization, also through an interactive website. For categorization, we present a benchmark taxonomy for well-defined characterization of benchmarks.

Benchmarking↗