Results for “User interface” — Page 61

DOE OSTI2016

SU-F-T-139: Meeting the Challenges of Quality Control in the TOPAS Monte Carlo Simulation Toolkit for Proton Therapy

Purpose: Monte Carlo particle transport simulation (MC) codes have become important tools in proton therapy and biology, both for research and practice. TOPAS is an MC toolkit serving users worldwide (213 licensed users at 95 institutions in 21 countries). It provides unprecedented ease in 4D placement of geometry components, beam sources and scoring through its user-friendly and reproducible parameter file interface. Quality control (QC) of stochastic simulation software is inherently difficult, and the versatility of TOPAS introduces additional challenges. But QC is vital as the TOPAS development team implements new features, addresses user feedback and reacts to upgrades of underlying software (i.e. Geant4). Methods: Whenever code is committed to our repository, over 50 separate module tests are automatically triggered via a continuous integration service. They check that the various module options execute successfully and that their results are statistically consistent with previous reference values. Prior to each software release, longer end-to-end tests automatically validate TOPAS against experimental data and a TOPAS benchmark. These include simulating multiple properties of spread-out Bragg peaks, validating nuclear models, and searching for differences in patient simulations. Results: Continuous integration has proven effective in catching regressions at the time they are introduced, particularly when implementing new features that involve refactoring code (e.g. multithreading and ntuple output). Code coverage statistics highlight untested portions of code and guide development of new tests. The various end-to-end tests demonstrate that TOPAS accurately describes the physics of proton therapy within clinical tolerances. Conclusion: The TOPAS QC strategy of frequent short tests and pre-release long tests has led to a more reliable tool. However, the versatility of TOPAS makes it difficult to predict how users might combine different modules, and so QC ultimately remains a partnership between the developer and the user. This work was funded by National Cancer Institute grant R01 CA 140735.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

CMS distributed data analysis with CRAB3

The CMS Remote Analysis Builder (CRAB) is a distributed workflow management tool which facilitates analysis tasks by isolating users from the technical details of the Grid infrastructure. Throughout LHC Run 1, CRAB has been successfully employed by an average of 350 distinct users each week executing about 200,000 jobs per day.CRAB has been significantly upgraded in order to face the new challenges posed by LHC Run 2. Components of the new system include 1) a lightweight client, 2) a central primary server which communicates with the clients through a REST interface, 3) secondary servers which manage user analysis tasks and submit jobs to the CMS resource provisioning system, and 4) a central service to asynchronously move user data from temporary storage in the execution site to the desired storage location. Furthermore, the new system improves the robustness, scalability and sustainability of the service.Here we provide an overview of the new system, operation, and user support, report on its current status, and identify lessons learned from the commissioning phase and production roll-out.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A General Method for Estimating Zonal Transmission Interface Limits from Nodal Network Data: Preprint

Capacity expansion models for the electric power system often employ zonal (rather than nodal) resolution, necessitating estimates of aggregate power transfer limits across the interfaces between model zones. Interface limits between planning areas are sometimes published, but they are not generalizable to arbitrary zone shapes. There is thus a need for a reproducible method for estimating interface transfer limits (ITLs) between user-defined zones directly from nodal transmission system data. Here, we present a simple method for estimating ITLs using a DC power flow approximation via the power transfer distribution factor (PTDF) matrix. Linear optimization is performed to identify the distribution of power flows that maximizes the total flow on interface-crossing lines, subject to individual line ratings, limits on bus injection/withdrawal, and the relationships among flows, injections, and withdrawals imposed by the PTDF matrix. We demonstrate the application of the method on a 134-zone ~65000-bus system, and we explore the influence of flow direction, contingency level, and zone size on the estimated ITLs. There is significant heterogeneity in the ratio of the ITL to the sum of interface-crossing line ratings, which highlights the importance of accounting for the physical constraints on power flows imposed by Kirchhoff's laws when estimating zonal ITLs.

17 WIND ENERGY↗

DOE OSTI2017

Simplified Interface to Complex Memory Hierarchies 1.x

Memory systems are expected to get evermore complicated in the coming years, and it isn't clear exactly what form that complexity will take. On the software side, a simple, flexible way of identifying and working with memory pools is needed. Additionally, most developers seek code portability and do not want to learn the intricacies of complex memory. Hence, we believe that a library for interacting with complex memory systems should expose two kinds of abstraction: First, a low-level, mechanism-based interface designed for the runtime or advanced user that wants complete control, with its focus on simplified representation but with all decisions left to the caller. Second, a high-level, policy-based interface designed for ease of use for the application developer, in which we aim for best-practice decisions based on application intent. We have developed such a library, called SICM: Simplified Interface to Complex Memory.

Lang, Michael↗

DOE OSTI2017

Simplified Interface to Complex Memory Hierarchies 1.x

Memory systems are expected to get evermore complicated in the coming years, and it isn't clear exactly what form that complexity will take. On the software side, a simple, flexible way of identifying and working with memory pools is needed. Additionally, most developers seek code portability and do not want to learn the intricacies of complex memory. Hence, we believe that a library for interacting with complex memory systems should expose two kinds of abstraction: First, a low-level, mechanism-based interface designed for the runtime or advanced user that wants complete control, with its focus on simplified representation but with all decisions left to the caller. Second, a high-level, policy-based interface designed for ease of use for the application developer, in which we aim for best-practice decisions based on application intent. We have developed such a library, called SICM: Simplified Interface to Complex Memory.

Lang, Michael↗

DOE OSTI2017

obtain3D

This computer code uses the concept of the parallax to compute the x, y and z coordinates of points found using transmission electron microscopy (TEM), or any transmission imaging technique, using two images, each taken at a different perspective of the region containing the points. Points correspond, but are not limited, to the center of cavities or precipitates, positions of irradiation black dot damage, positions along a dislocation line, or positions along where an interface meets a free surface. The code allows the user to visualize the features containing the points in three dimensions. Features can include dislocations, interfaces, cavities, precipitates, inclusions etc. The x, y and z coordinates of the points are output in a text file as well. The program can also combine the x, y and z coordinates of the points with crystallographic directional information from diffraction pattern(s) to calculate dislocation line directions and interface plane normals.

Eftink, Benjamin Paul↗

DOE OSTI2018

Global-Address Networking (GASNet-1) Library

GASNet is a language-independent, networking middleware layer that provides network-independent, high-performance communication primitives including Remote Memory Access (RMA) and Active Messages (AM). It has been used to implement parallel programming models and libraries such as UPC, Co-Array Fortran, Titanium, Legion, Chapel, and many others. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness. GASNet stands for "Global-Address Space Networking".

SciDAC↗

DOE OSTI2018

Global-Address Space Networking for Exascale

GASNet-EX is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of Partitioned Global Address Space (PGAS) runtime systems and other alternative models in future exascale machines. The library is an evolution of the popular GASNet communication system, building upon over 15 years of lessons learned. GASNet is a language-independent, networking middleware layer that provides network-independent, high-performance communication primitives including Remote Memory Access (RMA) and Active Messages (AM). It has been used to implement parallel programming models and libraries such as UPC, Co-Array Fortran, Titanium, Legion, Chapel, and many others. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness. GASNet stands for "Global-Address Space Networking".

ECP↗

DOE OSTI2017

GASNet Specification, v1.8.1

GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages and libraries such as UPC, UPC++, Co-Array Fortran, Legion, Chapel, and many others. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness. GASNet stands for "Global-Address Space Networking".

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Dosimetry Processor v1.0 User's Manual

The following discussion contains a detailed description of how to interface and operate Dosimetry Processor v1.0 software application. It describes the input required from the user to process dosimetry and actions to take for troubleshooting.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Improving FERRY: Visualization, Refactoring, and Testing

The Frontier Experiment RegistRY System (FERRY) is a metadata database that contains information about employees, the groups and experiments they belong to, and grid mapping and quota management for the Fermi National Accelerator Laboratory. It is predominantly used to acquire user information. FERRY is accessed through the use of APIs (Application Programming Interface), shown in Figure 1. Corresponding attributes are then displayed for the user in JSON (Java Script Object Notation) format. The goal of this project has been to build upon and improve aspects of FERRY. Including the refactoring of the code, building a visual interface, and creating a testing system for FERRY’s APIs.

Segura, Antonio Thomas↗

DOE OSTI2025

BOPTest As a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.

Paul, Lazlo↗

DOE OSTI2025

BOPTEST as a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.

Paul, Lazlo↗

DOE OSTI2024

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

REopt Lite User Manual

REopt Lite evaluates the economic viability of grid-connected solar photovoltaics, wind, combined heat and power, and electric and thermal storage at commercial and small industrial sites. It allows building owners to identify the system sizes and dispatch strategies that minimize the site’s life cycle cost of energy. REopt Lite also estimates the amount of time on-site generation and storage can sustain the site's critical load during a grid outage and allows the user the choice of optimizing for energy resilience. It is primarily used to inform project development decisions and to support research on the factors that drive project feasibility for market development and policy analysis. It is available through a web interface, application programing interface, and open-source code. This user manual provides an overview of the model, including its capabilities and typical applications; inputs and outputs; economic calculations; technology descriptions; and model parameters, variables, and equations. The model is highly flexible and is continually evolving to meet the needs of each analysis. Therefore, this report is not an exhaustive description of all capabilities, but rather a summary of the core components of the model.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Automated extraction of interfacial dislocations and disconnections from atomistic data

Here we introduce Interfacial Line Defect Analysis (ILDA), a method for identifying and extracting interfacial dislocations and disconnections with little-to-no input from the user on the nature of the interface. By simply providing the orientations and coherency strains for the crystals in a coherent reference state of the interface, ILDA provides exact Burgers vectors. Alternatively, these orientations and strains can be estimated using local atomic deformation gradients, making ILDA fully automated and providing estimated Burgers vectors. ILDA also determines the step height associated with each defect line segment, in case the associated defect is a disconnection. The heart of the method is the identification of atoms residing at co-incidence sites between the two crystals and the construction of a surface mesh connecting these sites that is used to compose Burgers circuits and insert defect line segments. We demonstrate the performance of ILDA in two test cases: a twist grain boundary and a phase boundary.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Web-based methods for X-ray and photoelectron spectroscopies

We present a simplified web-based application for simulating x-ray and photoelectron spectra of transition metals, built around the notion that web-based applications lower the bar for novice users. The application provides a simple interface to simulate x-ray absorption spectroscopy, resonant inelastic x-ray scattering, and angle-resolved photoemission spectroscopy, incorporating the effects of local electronic interactions, which give rise to multiplets, spin-orbit coupling, crystal field effects, and ligand hybridization/charge transfer. Results can be obtained that highlight the key role of photon polarization.

36 MATERIALS SCIENCE↗

DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗