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At least 181 records · Page 10

Developments in Performance and Portability for MadGraph5_aMC@NLO

Event generators simulate particle interactions using Monte Carlo techniques, providing the primary connection between experiment and theory in experimental high energy physics. These software packages, which are the first step in the simulation worflow of collider experiments, represent approximately 5 to 20% of the annual WLCG usage for the ATLAS and CMS experiments. With computing architectures becoming more heterogeneous, it is important to ensure that these key software frameworks can be run on future systems, large and small. In this contribution, recent progress on porting and speeding up the Madgraph5_aMC@NLO event generator on hybrid architectures, i.e. CPU with GPU accelerators, is discussed. The main focus of this work has been in the calculation of scattering amplitudes and "matrix elements", which is the computational bottleneck of an event generation application. For physics processes limited to QCD leading order, the code generation toolkit has been expanded to produce matrix element calculations using C++ vector instructions on CPUs and using CUDA for NVidia GPUs, as well as using Alpaka, Kokkos and SYCL for multiple CPU and GPU architectures. Performance is reported in terms of matrix element calculations per time on NVidia, Intel, and AMD devices. The status and outlook for the integration of this work into a production release usable by the LHC experiments, with the same functionalities and very similar user interfaces as the current Fortran version, is also described.

Valassi, Andrea↗

PyXAS – an open-source package for 2D X-ray near-edge spectroscopy analysis

In the synchrotron X-ray community, X-ray absorption near-edge spectroscopy (XANES) is a widely used technique to probe the local coordination environment and the oxidation states of specific elements within a sample. Although this technique is usually applied to bulk samples, the advent of new synchrotron sources has enabled spatially resolved versions of this technique (2D XANES). This development has been extremely powerful for the study of heterogeneous systems, which is the case for nearly all real applications. However, associated with the development of 2D XANES comes the challenge of analyzing very large volumes of data. As an example, a single 2D XANES measurement at a synchrotron can easily produce ~106 spatially resolved XANES spectra. Conventional manual analysis of an individual XANES spectrum is no longer feasible. Here, a software package is described that has been developed for high-throughput 2D XANES analysis. A detailed description of the software as well as example applications are provided.

25 ENERGY STORAGE↗

CiteSoft_Py

There is a need to provide a way for dev-users (Scientists, Engineers, and other Software Developers) to get credit (citations) when they contribute to an important software package - particularly a large package that is already established. Various solutions (including cross package) solutions do exist, but a simple standard format that can work between multiple packages and multiple languages in a modular way is not widely available. CiteSoft_py is a python implementation of CiteSoft. CiteSoft is a plain text standard consisting of a format and a protocol that exports the citations for the end-users for whichever softwares they have used. CiteSoft has been designed so that software dev-users can rely upon it regardless of coding language or platform, and even for cases where multiple codes are working in a coupled manner. The CiteSoft_py implementation includes python decorators to make wrappers for facile use. The purpose is that when dev-users (scientists, engineers and professional programmers) contribute to a collaborative software project, that the appropriate citations (e.g., journal article, conference proceeding) are provided to the end-user. The end-user does not need to know how to use a command line interface, API, etc.

Savara, Aditya↗

Mantaray: A Rust Package for Ray Tracing Ocean Surface Gravity Waves

Ocean surface gravity waves are an important component of air-sea interaction, influencing energy, momentum, and gas exchanges across the ocean-atmosphere interface. In specific applications such as refraction by ocean currents or bathymetry, ray tracing provides a computationally efficient way to gain insight into wave propagation. In this paper, we introduce Mantaray, an open-source software package implemented in Rust, with a Python interface, that solves the ray equations for ocean surface gravity waves. Mantaray is designed for performance, robustness, and ease of use. The package is modular to facilitate further development and can currently be applied to both idealized and realistic wave propagation problems (Fig. 1).

16 TIDAL AND WAVE POWER↗

Hydropower Biological Evaluation Toolset (HBET) Version 3.0: User Guide

The Hydropower Biological Evaluation Tools (HBET) software package, developed by Pacific Northwest National Laboratory (PNNL), is designed to assemble, organize, and process data collected by Sensor Fish and live fish. HBET enable users to characterize the hydraulic conditions of hydropower structures and estimate fish injury and mortality rates from various stressors. Future updates of the software may support other technologies, such as bead tracking in physical models and computational fluid dynamics. The HBET program can be customized to analyze different hydraulic applications, including turbines, spillways, weirs, pumped storage, and other user-defined functions, and therefore, help researchers, turbine designers, hydropower operators, and regulators better evaluate hydropower structures regarding their environmental sustainability and cost-effectiveness. Added content to the user guide about the new feature for predicting absolute injury rates.

13 HYDRO ENERGY↗

Modeling receiver flux of commercial power tower concentrating solar power plants using ray tracing: a round-robin comparison of SolTrace, Solstice, and TieSOL

This study presents a multi-stage, cross-validation comparison of three software packages for Monte Carlo ray tracing (MCRT) applied to central tower concentrating solar power (CSP) systems. The three packages evaluated are: (1) SolTrace, an open-source tool developed by the National Renewable Energy Laboratory (NREL); (2) Solstice, an open-source program created by CNRS-PROMES and Meso-Star, with enhancements for CSP applications (called solsticepy) from the Australian National University; and (3) TieSOL, a commercial software developed by Tietronix. This investigation extends previous ray tracing comparisons by incorporating models of multi-facet heliostats within a commercial-scale solar field, taking into account zoned focal lengths and canting configurations. Receiver flux distributions were compared across the tools using a series of case studies, including single-heliostat scenarios, isolated blocking situations, and comprehensive full-field simulations. The case studies were designed to diagnose differences across the models at varying levels of complexity, and to identify and resolve discrepancies as additional parameters were introduced. Key factors examined in the analysis include sun positions, heliostat location, facet and canting focus, and aimpoint strategies. The comparison aims to improve the accuracy and reliability of these tools while providing benchmark cases for validating future optical modeling tools.

14 SOLAR ENERGY↗

Livermore tomography tools: Accurate, fast, and flexible software for tomographic science

Livermore Tomography Tools (LTT) is a customizable scientific software package that enables a broad range of research and development efforts into computed tomography (CT). Here, it was developed to process x-ray and neutron CT data accurately and rapidly from raw detector counts to reconstructed volumes with the flexibility to handle many special cases. LTT fulfills long-term CT software goals to provide quantitatively accurate results reported in physical units (e.g., mm -1 or cm -1 ) while exploiting all available computational advantages to maximize speed. Written in C/C++ with support for multiple CPUs and GPUs, LTT runs on many computing platforms (Linux/Unix, Windows, and Mac; laptops to supercomputers). As a result, LTT can:process data acquired from various custom-built and commercially available CT scanners, model and simulate x-ray and neutron interactions to encourage algorithm prototyping, and allow for rapid insertion of the latest algorithms.We describe LTT’s software architecture, user interfaces, and its 88 algorithms (as of this writing) for pre-processing, reconstruction, post-processing, and simulation that support many scanner geometries (parallel-, fan-, cone-beam, and custom). Several applications are presented that illustrate LTT’s accuracy, speed, and flexibility relative to other solutions.

36 MATERIALS SCIENCE↗

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform ( RPX ) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting Instability and the Effect of Wind Loading on Single-Axis Trackers

As PV modules continue to trend toward larger, thinner, and more flexible forms they grow more susceptible to damage from dynamic wind loading. As a result, understanding the impact of wind on PV systems, particularly when mounted on solar-tracking hardware, and identifying robust, stable array layouts and stow strategies is becoming increasingly important for the PV community. In our ongoing DuraMAT project, we are developing an open-source software package, PVade (PV aerodynamic design engineering), to simulate the cascading fluid-structure interaction that occurs within solar-tracking arrays to enable researchers to test hardware, layout, and tracker control changes, leading to enhanced stability and a reduction in wind-driven damage. We will give an overview of the PVade software, highlighting recent user-interface and algorithm developments, before presenting the latest outcomes from our ongoing validation campaign in which we analyze and compare with experimental data obtained from a DuraMAT 1 project. From there, we will present simulated results from a larger, multi-row array and highlight relationships between varying tracker angles and stability as measured by different experimentally validated metrics.

fluid structure interaction↗

A Simulation and Optimization Framework for Managing Wind-Driven Loading on PV Systems

As PV modules continue to trend toward larger, thinner, and more flexible forms they grow more susceptible to damage from dynamic wind loading. As a result, understanding the impact of wind on PV systems, particularly when mounted on solar-tracking hardware, and identifying robust, stable array layouts and stow strategies is becoming increasingly important for the PV community. We are developing an open-source software package, PVade (PV aerodynamic design engineering), to simulate the cascading fluid-structure interaction that occurs within solar-tracking arrays to enable researchers to test hardware, layout, and tracker control changes, leading to enhanced stability and a reduction in wind-driven damage. We will give an overview of the PVade software and present the latest outcomes from our ongoing validation campaign in which we compare statistical structural responses with field data. From there, we will present simulated results from a larger, multi-row array and highlight the effect of varying tracker angles on stability as measured by both acceleration and deformation, focusing on the stability differences between positive and negative tilt angles.

fluid structure interaction↗

rNets: a standalone package to visualize reaction networks

In the study of chemical processes, visualizing reaction networks is pivotal for identifying crucial compounds and transformations. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity. Alternatives capable of leading with complexity include graph methods, but they are not user-friendly, lacking simplicity and modularity, which hinders their integration with widely-used research software. This work introduces rNets an innovative tool designed for the efficient visualization of reaction networks with a user-friendly interface, modularity, and seamless integration with existing software packages. The effectiveness of rNets is demonstrated through its application in analyzing three catalytic reactions, showcasing its potential to significantly enhance research both in homogeneous and heterogeneous catalysis fields. This tool not only simplifies the visualization process but also opens new avenues for exploring complex reaction networks in diverse research contexts.

Pablo-García, Sergio↗

Simulating Wind-Driven Loading on PV Systems

As PV modules continue to trend toward larger, thinner, and more flexible forms they grow more susceptible to damage from dynamic wind loading. As a result, understanding the impact of wind on PV systems, particularly when mounted on compliant solar-tracking hardware, and identifying robust, stable array layouts and stow strategies is becoming increasingly important for the PV community. We are developing an open-source software package, PVade (PV aerodynamic design engineering), to simulate the cascading fluid-structure interaction that occurs within single-axis, solar-tracking arrays to enable researchers to test hardware, layout, and tracker control changes, leading to enhanced stability and a reduction in wind-driven damage. We will give an overview of the PVade software and present the latest outcomes from our ongoing validation campaign in which we compare time series and statistical structural responses with field data. From there, we will present simulated results from a larger, multi-row array and highlight the effect of varying tracker angles on stability and the differences between positive and negative tilt angles.

fluid↗

Toward Polydisperse Flows With MFIX-EXA

In the presence of large size disparities, single-grid neighbor search algorithms lead to inflated neighbor lists that significantly degrade the performance of Lagrangian particle solvers. If Eulerian–Lagrangian (EL) frameworks are to remain performant when simulating realistic systems, improved neighbor detection approaches must be adopted. To this end, we consider the application of a multigrid neighbor search (MGNS) algorithm in the mfix-exa software package, an exascale EL solver built upon the AMReX library. Here, details regarding the implementation and verification of MGNS are provided along with speedup curves for a bidisperse mixing layer. MGNS is shown to yield up to 15$\times$ speedup on CPU and 6$\times$ speedup on GPU for the problems considered here. The mfix-exa software is then validated for a variety of polydisperse flows. Finally, a brief discussion is given for how dynamic MGNS may be completed, with application to spatially varying particle size distributions.

42 ENGINEERING↗

Numerical methods and hypoexponential approximations for gamma distributed delay differential equations

Abstract Gamma distributed delay differential equations (DDEs) arise naturally in many modelling applications. However, appropriate numerical methods for generic gamma distributed DDEs have not previously been implemented. Modellers have therefore resorted to approximating the gamma distribution with an Erlang distribution and using the linear chain technique to derive an equivalent system of ordinary differential equations (ODEs). In this work, we address the lack of appropriate numerical tools for gamma distributed DDEs in two ways. First, we develop a functional continuous Runge–Kutta (FCRK) method to numerically integrate the gamma distributed DDE without resorting to Erlang approximation. We prove the fourth-order convergence of the FCRK method and perform numerical tests to demonstrate the accuracy of the new numerical method. Nevertheless, FCRK methods for infinite delay DDEs are not widely available in existing scientific software packages. As an alternative approach to solving gamma distributed DDEs, we also derive a hypoexponential approximation of the gamma distributed DDE. This hypoexponential approach is a more accurate approximation of the true gamma distributed DDE than the common Erlang approximation but, like the Erlang approximation, can be formulated as a system of ODEs and solved numerically using standard ODE software. Using our FCRK method to provide reference solutions, we show that the common Erlang approximation may produce solutions that are qualitatively different from the underlying gamma distributed DDE. However, the proposed hypoexponential approximations do not have this limitation. Finally, we apply our hypoexponential approximations to perform statistical inference on synthetic epidemiological data to illustrate the utility of the hypoexponential approximation.

97 MATHEMATICS AND COMPUTING↗

Microwave Cavity Simulation Using Ansys HFSS

The design of microwave cavity detectors for axion dark matter research is often accomplished using advanced full-wave electromagnetic simulation software tools. These tools provide a cost-effective approach to evaluate a wide variety of cavity configurations, frequency tuning mechanisms, and conductive or dielectric materials and coatings. One simulation software package used for this application is Ansys High Frequency Structure Simulator (HFSS), which is based upon the well-established finite element method. HFSS includes numerous features useful for microwave cavity design such as parametric geometry modeling, adaptive meshing algorithm, curvilinear mesh elements, driven modal and eigenmode matrix solvers, and optimization algorithms. This paper describes the use of the HFSS software to simulate microwave cavities for axion haloscope detectors, with an example tutorial for a cylindrical cavity. Excellent agreement between the simulated and analytical results is shown for the resonant frequency, quality factor, and form factor.

Ansys HFSS, Cavity simulation, finite element mode↗

MPACT Safeguards Modeling: FY25 Update

Sandia National Laboratories develops and maintains several open-source software packages to support material accountancy analyses. This includes the Material Accountancy Performance Indicator Toolkit (MAPIT), the Fissile Facility Flow Modeler (F3M) and the Separation and Safeguards Performance Model Library (SSPM-L). MAPIT is responsible for performing statistical safeguards analyses on bulk and itemized data from nuclear fuel cycle facilities and can operate on real or synthetic data. MAPIT is the only open-source software for such analyses. F3M is a library of modules, built in MATLAB Simulink, that contain pre made blocks to represent different generic fuel cycle processes. These blocks can be used together in a modular fashion to represent and simulate nuclear fuel cycle processes with the goal of improving facility-level accountancy during the design phase. F3M is also an open-source library. Finally, the SSPM-L library is a series of completed models built from F3M. The library includes facility models such as a generic PUREX facility and a fuel fabrication facility. The SSPM-L library is not open source, but is available to collaborators with a relevant use case. These tools include modeling and simulation pipelines to simulate nuclear fuel cycle facilities and the underlying software needed to simulate measurement uncertainty and perform statistical analyses. Together, these tools can perform end-to-end nuclear material accountancy analyses. This report documents the various improvements made to these tools in FY25. Specifically, we added new statistical test, new statistical modeling capabilities, new fuel cycle facility models, and launched a new open-source model component library.

97 MATHEMATICS AND COMPUTING↗

Better understanding and prediction of antiviral peptides through primary and secondary structure feature importance

The emergence of viral epidemics throughout the world is of concern due to the scarcity of available effective antiviral therapeutics. The discovery of new antiviral therapies is imperative to address this challenge, and antiviral peptides (AVPs) represent a valuable resource for the development of novel therapies to combat viral infection. We present a new machine learning model to distinguish AVPs from non-AVPs using the most informative features derived from the physicochemical and structural properties of their amino acid sequences. To focus on those features that are most likely to contribute to antiviral performance, we filter potential features based on their importance for classification. These feature selection analyses suggest that secondary structure is the most important peptide sequence feature for predicting AVPs. Our Feature-Informed Reduced Machine Learning for Antiviral Peptide Prediction (FIRM-AVP) approach achieves a higher accuracy than either the model with all features or current state-of-the-art single classifiers. Understanding the features that are associated with AVP activity is a core need to identify and design new AVPs in novel systems. The FIRM-AVP code and standalone software package are available at https://github.com/pmartR/FIRM-AVP with an accompanying web application at https://msc-viz.emsl.pnnl.gov/AVPR.

59 BASIC BIOLOGICAL SCIENCES↗

hIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described by partial differential equations (PDEs) remains prohibitive with black-box Markov chain Monte Carlo (MCMC) methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two complementary libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems across a broad spectrum of scientific and engineering disciplines. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods available in the integrated software on several high-dimensional Bayesian inverse problems. These include problems characterized by both linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large (~ 50×) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log-posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

97 MATHEMATICS AND COMPUTING↗