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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A Python Tool for Reconstructing MCNP6 Particle Histories from an HDF5 PTRAC File [Slides]

A Python tool for converting the MCNP6 HDF5 PTRAC file to a list of Python trees is presented. The particle trees store MCNP6 simulated events for each history using parent-child relationships, which ensures that branching processes are accurately reproduced. A variety of post-processing scripts are presented and used in conjunction with the Python particle trees to make special tallies that are currently not available in the MCNP6 software and visualize the particle tracks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Progress Towards International GNDS Adoption [Slides]

This presentation includes a GNDS quick overview. Libraries are increasingly available in GNDS as well as ENDF-6, Multiple evaluation / processing / checking / visualization codes have begun to support GNDS. LLNL codes FUDGE and GIDIplus are open-source tools for creating, processing and using GNDS.

Generalised Nuclear Database Structure (GNDS)↗
DOE OSTI2015

Long-term Results of the UCSF-LBNL Randomized Trial: Charged Particle With Helium Ion Versus Iodine-125 Plaque Therapy for Choroidal and Ciliary Body Melanoma

Purpose: Relevant clinical data are needed given the increasing national interest in charged particle radiation therapy (CPT) programs. Here we report long-term outcomes from the only randomized, stratified trial comparing CPT with iodine-125 plaque therapy for choroidal and ciliary body melanoma. Methods and Materials: From 1985 to 1991, 184 patients met eligibility criteria and were randomized to receive particle (86 patients) or plaque therapy (98 patients). Patients were stratified by tumor diameter, thickness, distance to disc/fovea, anterior extension, and visual acuity. Tumors close to the optic disc were included. Local tumor control, as well as eye preservation, metastases due to melanoma, and survival were evaluated. Results: Median follow-up times for particle and plaque arm patients were 14.6 years and 12.3 years, respectively (P=.22), and for those alive at last follow-up, 18.5 and 16.5 years, respectively (P=.81). Local control (LC) for particle versus plaque treatment was 100% versus 84% at 5 years, and 98% versus 79% at 12 years, respectively (log rank: P=.0006). If patients with tumors close to the disc (<2 mm) were excluded, CPT still resulted in significantly improved LC: 100% versus 90% at 5 years and 98% versus 86% at 12 years, respectively (log rank: P=.048). Enucleation rate was lower after CPT: 11% versus 22% at 5 years and 17% versus 37% at 12 years, respectively (log rank: P=.01). Using Cox regression model, likelihood ratio test, treatment was the most important predictor of LC (P=.0002) and eye preservation (P=.01). CPT was a significant predictor of prolonged disease-free survival (log rank: P=.001). Conclusions: Particle therapy resulted in significantly improved local control, eye preservation, and disease-free survival as confirmed by long-term outcomes from the only randomized study available to date comparing radiation modalities in choroidal and ciliary body melanoma.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Modeling City Building Stock for Large-Scale Energy Efficiency Improvements using CityBES

Buildings in San Francisco consumed 52% of total primary energy. Improving building energy efficiency is one of the key strategies cities are adopting towards their energy and climate goals. Urban building energy models (UBEM) can support city managers to evaluate and prioritize energy conservation measures for investment and to design effective incentive and rebate programs. This paper introduces methods to develop a standardized dataset of city building stock, and it demonstrates the use of a UBEM tool, City Building Energy Saver (CityBES), for an urban-scale energy retrofit analysis of building stock in the city of San Francisco. CityBES is an open web-based data and computing platform providing city-scale building energy modeling and performance visualization and benchmarking. CityBES utilizes an international standard CityGML to represent the three-dimensional building stock in cities. As an application example, 940 office and retail buildings in six districts of northeast San Francisco were modeled and analyzed with CityBES to evaluate energy savings for five selected measures. The analysis found that replacing existing lighting with LED and adding an air economizer to HVAC systems are cost-effective measures with combined savings per building between 17% to 31%. The CityBES retrofit analysis feature does not require users to have deep knowledge of building systems or building energy models, which helps overcome barriers for city managers and their consultants to adopt UBEM.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Combining Particle Tracking with Electromagnetic Radiation Showers: Merging GPT and Geant4 with Visualization

Field emitted electrons can seriously affect the operation of high-field, high-duty factor electron accelerators. Accelerated field emission can result in high average power beams which can radiation damage beamline components. In addition, localized losses generate thermal hot spots whose outgassing degrades the ultra-high vacuum required in photoinjectors and cryomodules. However, despite their importance, the effects of field emission are rarely included in the design and engineering of electron injectors. This work attempts to remedy this situation by combining two well-known and well-documented programs, GPT and Geant4, to track electrons and their losses in an injector beamline. This paper describes a system of programs which simulates electron paths and losses along the beamline. In addition, the tracking results can be zoomed and panned along and about the beampipe envelope using an open-source 3D CAD program. The scattering albedo calculations of the combined program, GPT-Geant4, are shown to be in good agreement with the literature albedos. The paper concludes with a dark current simulation for the LCLS-II injector from the cathode to the collimator at 1.5 m from the cathode.

Dowell, David H.↗
DOE OSTI2024

Large language model evaluation for high–performance computing software development

We apply AI-assisted large language model (LLM) capabilities of GPT-3 targeting high-performance computing (HPC) kernels for (i) code generation, and (ii) auto-parallelization of serial code in C ++, Fortran, Python and Julia. Our scope includes the following fundamental numerical kernels: AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG, and language/programming models: (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). Kernel implementations are generated using GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code given simple + + prompt variants. To quantify and compare the generated results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. For auto-parallelization, we use ChatGPT interactively giving simple prompts as in a dialogue with another human including simple “prompt engineering” follow ups. Results suggest that correct outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general-purpose Python can benefit from adding language keywords, while Julia prompts perform acceptably well for its Threads and CUDA.jl programming models. Finally, we expect to provide an initial quantifiable point of reference for code generation in each programming model using a state-of-the-art LLM. Overall, understanding the convergence of LLMs, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

PymePix : a python library for SPIDR readout of Timepix3

PymePix is a new Python 3 library that provides control and acquisition for the Timepix3-SPIDR hardware. The rich set of data-structures and intuitive routines reduces time and coding effort to quickly configure, acquire, and visualize data from Timepix3. The highly extensible high-performance data-pipeline allows for alteration of the Timepix3 datastream into a form that is convinient for the user. This library is intended to be easily inserted into a standard scientific software stack as well as to allow for more direct interaction of Timepix3 with interactive flavors of Python. Included with the library are two example programs using PymePix: pymepix-acq is a command line control and acquisition program that can capture UDP packets and decode them into pixels and triggers. The second is pymepixviewer, an online control and data-acquisition program for general use, but with features geared toward mass-spectroscopy and ion imaging.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Using the Criticality Accident Alarm System modeling capabilities in SCALE [Slides]

The following is a summary of advice for CAAS modeling in SCALE. Refer to the SCALE Criticality Safety and Radiation Shielding training slides or to the SCALE manual for exact syntax. Use a mesh for the fission source that is the most adequate for the problem to solve (coarse/fine). Don’t spend unnecessary resources; simplify the model if it does not impact the final results of interest. Be careful to deactivate secondary fissions in MAVRIC or the calculation may never end. Check that k eff and $\overline{\upsilon}$ calculated results are logical. Between KENO and MAVRIC, cross section libraries, materials, geometry, and mesh grid can be the same or different. Iterative calculations are usually complex problems that need variance reduction. It will be hard to find the best solving parameters in the first attempt; expert judgement is needed. Check each step separately. Use Fulcrum to visualize fission source, mesh source, and spatial/energy distributions to find potential errors or impactful imprecisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Distributions of the Mean for Lognormally Distributed Data - 19427

In environmental sciences, a distribution of the mean is often needed for right-skewed data. For example, risk assessments are often based on distributions of the mean to obtain upper confidence limits (UCLs) for analyte concentrations, and, in probabilistic performance assessment (PPA) models, parameters are given distributions rather than deterministic values, and they are usually given distributions of their mean rather than the population distributions to account for the large spatial and temporal domains to which they are applied. How this distribution of the mean is developed depends on the characteristics of the parameter's full distribution and how the parameter relates to its use. In this presentation, I will discuss the implications of a right skew in distribution development. Parameters may vary over orders of magnitude and/or may be right-skewed. The material property of saturated hydraulic conductivity, Ks, is a prime example of such a parameter. Right-skewed parameters are often assumed to follow lognormal distributions. If X follows a lognormal distribution, then log(X) follows a normal distribution. For some right-skewed parameters, practitioners go back and forth between the two forms of the data depending on their needs. For example, it may be preferred to use the untransformed version of X in a model or equation, but it is easier to visualize the parameter values on a logarithmic scale. However, distribution development for the average value of the parameter will differ depending on whether X or log(X) is modeled. This difference is due to Jensen's Inequality, a theorem which states that the expected value of a concave function of a variable is less than or equal to the same function of the expected value of the variable; a logarithm is a concave function. In other words, the mean of log(X) is always less than or equal to the log of the mean of X and therefore the mean estimated from a distribution based on log(X) is less than or equal to the mean estimated from a distribution based on X. If a parameter is naturally considered on a log scale by subject matter experts, then distributions developed for the mean of log(X) may be more consistent with the use of the parameters in the literature than distributions developed for X. The statistical decisions of distribution development will be discussed within the context of right-skewed, lognormal data. These issues include method-of-moments versus maximum likelihood estimation of the distribution parameters and the use of bootstrapping to aid in the visualization of a distribution of the mean. The details surrounding Jensen's Inequality will be explained and visualized within the context of distribution development of a right-skewed parameter such as saturated hydraulic conductivity. (authors)

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

The Case for Artificial Intelligence

The emerging era of artificial intelligence will be beneficial to society and is worth embracing, says Argonne’s Marius Stan, Program Lead for Intelligent Materials Design. Artificial intelligence is playing a significant role in defining new research methods that bring us to resolution or discovery more quickly than ever before. Argonne is using or developing many of these technologies as AI extends to new branches of science and technology, sprouting new buds that represent various facets of human function and cognition — from learning to language processing to visual recognition.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Software Development for Data Visualization and Analysis of PN-Diodes & MOSFET Devices

The U.S. Department of Energy has a broad mission to ensure the nation’s security by addressing ongoing environmental challenges, developing novel energy production technologies, and mitigating nuclear security concerns. These efforts benefit from developing more effective semiconductor materials and devices. The research discussed in this report aims to further the development of these new electronics by improving implementations of vertical device structures, which offer theoretically better performance compared to lateral structures. Specifically, it reviews the background and development of a new and easy-to-use program for data processing and analysis from experiments run on vertical gallium nitride power devices. Current vertical structures fall short in critical performance metrics, such as On-Resistance and Breakdown Voltage, due to poor management of the device’s electric field. Junction termination extensions, or JTEs, are a field management technique that increases a device’s resilience to expected failure modes by controlling its surface electric fields. Each JTE design requires significant experimental validation, consisting of hundreds of tested devices, each outputting an enormous set of data points. The new software includes multiple methods of filtering large sets of device testing data to identify and remove flawed devices, automate device analyses, and provide statistical breakdowns for four metrics used to define the effectiveness of the JTE and the current carrying capacity of the device. These results can then be related back to fabrication techniques and device design, and in the future, be combined with processing simulations to further improve our understanding of the JTE mechanisms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

SU-E-J-266: A Pitfall of a Deformable Image Registration in Lung Cancer

Purpose: For four-dimensional (4D) planning and adaptive radiotherapy, deformable image registration (DIR) is needed and the accuracy is essential. We evaluated the accuracy of one free-downloadable DIR software library package (NiftyReg) and one commercial DIR software (MIM) in lung SBRT cancer patients. Methods: A rigid and non-rigid registrations were implemented to our in-house software. The non-rigid registration algorithm of the NiftyReg and MIM was based on the free-form deformation. The accuracy of the two software was evaluated when contoured structures to peak-inhale and peak-exhale 4DCT image data sets were measured using the dice similarity coefficient (DSC). The evaluation was performed in 20 lung SBRT patients. Results: In our visual evaluation, the eighteen cases show good agreement between the deformed structures for the peak-inhale phase and the peak-exhale phase structures (more than 0.8 DSC value). In the evaluation of the DSC in-house software, averaged DSC values of GTV and lung, heart, spinal cord, stomach and body were 0.862 and 0.979, 0.932, 0.974, 0.860, 0.998, respectively. As the Resultof the registration using the MIM program in the two cases which had less than 0.7 DSC value when analyzed using the in-house software, the DSC value were improved to 0.8. The CT images in a case with low DSC value shows the tumor was surrounded by the structure with the similar CT values, which were the chest wall or the diaphragm. Conclusion: Not only a free-downloadable DIR software but also a commercial software may provide unexpected results and there is a possibility that the results would make us misjudge the treatment planning. Therefore, we recommend that a commissioning test of any DIR software should be performed before clinical use and we should understand the characteristics of the software.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Havery Mudd 2014-2015 Computer Science Conduit Clinic. Final Report

Conduit, a new open-source library developed at Lawrence Livermore National Laboratories, provides a C++ application programming interface (API) to describe and access scientific data. Conduit’s primary use is for inmemory data exchange in high performance computing (HPC) applications. Our team tested and improved Conduit to make it more appealing to potential adopters in the HPC community. We extended Conduit’s capabilities by prototyping four libraries: one for parallel communication using MPI, one for I/O functionality, one for aggregating performance data, and one for data visualization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Novel Approaches and Technologies for Aging Management

As part of the application process for license renewal and subsequent license renewal, nuclear utilities must perform an evaluation to confirm that they have appropriately considered aging effects on plant structures, systems, components within the scope of the license renewal. This effort within the Light Water Reactor Sustainability program’s Risk-informed System Analysis pathway is focused on risk-informed and performance-based approaches for aging management of buried piping, specifically managing selective leaching degradation phenomena. Selective leaching is a commonly occurring aging and degradation mechanism in buried pipes at nuclear power plants. To better understand the extent of selective leaching and its effect on the health of buried components, the licensees currently rely on visual inspections and destructive examinations which require extraction of multiple buried components. This research explores technological solutions that may replace or supplement existing inefficient, costly, and labor-intensive methods used in aging management.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2018

Nuclear, Land marker for a Waste Isolation Site: International Architecture Competition - 18240

The design and construction of a nuclear waste marker must include many architectural considerations. Very little research has been conducted by architects to address this issue to date. Historically, the task of designating a nuclear waste site has been a discussion predominantly contained within the scientific and engineering communities. In an effort to engage architects within this dialogue, arch out loud hosted the NUCLEAR competition as an international, architectural investigation into the design of a nuclear waste site marker. The NUCLEAR competition asks participants to design a marker to designate the site of the Waste Isolation Pilot Plant (WIPP) located near Carlsbad, New Mexico. The marker will be meant to be a means of passive institutional controls (PICs) to deter inadvertent human intrusion upon the site and should last 10,000 years. The NUCLEAR competition defined the purpose of the nuclear waste site marker as a means to communicate the danger of inadvertent intrusion from future generations. The competition requires that entries must be both legible in communication and durable in their construction. The competition brief challenged participants to consider how customs and languages will evolve over time and to predict what motivations future generations might have for digging at the site. Other background information was provided about the site such as how waste was stored and how the unique geology of the site seals the waste. The 1993 Sandia National Laboratories report titled Expert Judgment on Markers to Deter Inadvertent Human Intrusion into the Waste Isolation Pilot Plant [1] was referenced along with the 1992 WIPP Land Withdrawal Act [2], interviews with WIPP scientists [3] involved with the WIPP PICs program and the Nuclear Energy Agency Records Knowledge and Memory working group. Competition participants were given digital 3-D Computer-Aided Design models for reference that included the underground storage portion of the site, existing buildings and the 16-square-mile site boundary identified in the 1992 WIPP Land Withdrawal Act [2]. This paper will: - Provide a detailed description of the submitted proposals including graphic analysis of the visualizations, diagrams, technical drawings, jury comments and statements. - Catalogue and identify the consistent themes within all submissions with possible categories including: 1) overall architectural form and language, 2) integration of written language and symbols within architecture, 3) use of technology and robotics, 4) construction methods and materials. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

SimCCS: An open-source tool for optimizing CO 2 capture, transport, and storage infrastructure

Commercial-scale carbon capture and storage (CCS) technology will involve deploying infrastructure on a massive and costly scale. This effort will require careful and comprehensive planning to ensure that capture locations, storage sites, and the dedicated CO 2 distribution pipelines are selected in a robust and cost-effective manner. Presented in 2009, SimCCS is an optimization model for integrated system design that enables researchers, stakeholders, and policy makers to design CCS infrastructure networks. SimCCS 2.0 is a complete, ground-up redesign that is now a portable software package, useable and shareable by the CCS research, industrial, policy, and public communities. SimCCS 2.0 integrates multiple new capabilities including a refined optimization model, novel candidate network generation techniques, and optional integration with high-performance computing platforms. Accessing user-provided CO 2 source, sink, and transportation data, SimCCS 2.0 creates candidate transportation routes and formalizes an optimization problem that determines the most cost-effective CCS system design. This optimization problem is further solved either through a high-performance computing interface, or through third-party software on a local desktop computing platform. Finally, SimCCS 2.0 employs an open-access geographic information system framework to enable analysis and visualization capabilities. SimCCS 2.0 is written in Java and is publicly available via GitHub to encourage collaboration, modification, and community development.

42 ENGINEERING↗
DOE OSTI2015

Simulator for an Accelerator-Driven Subcritical Fissile Solution System

LANL has developed a process to generate a progressive family of system models for a fissile solution system. This family includes a dynamic system simulation comprised of coupled nonlinear differential equations describing the time evolution of the system. Neutron kinetics, radiolytic gas generation and transport, and core thermal hydraulics are included in the DSS. Extensions to explicit operation of cooling loops and radiolytic gas handling are embedded in these systems as is a stability model. The DSS may then be converted to an implementation in Visual Studio to provide a design team the ability to rapidly estimate system performance impacts from a variety of design decisions. This provides a method to assist in optimization of the system design. Once design has been generated in some detail the C++ version of the system model may then be implemented in a LabVIEW user interface to evaluate operator controls and instrumentation and operator recognition and response to off-normal events. Taken as a set of system models the DSS, Visual Studio, and LabVIEW progression provides a comprehensive set of design support tools.

42 ENGINEERING↗