Open-source Release of CGMF and Integration into the MCNP6.3 Code
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Rising, Michael Evan↗
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PeleLMeX: an AMR Low Mach Number Reactive Flow Simulation Code without level sub-cycling
PeleLMeX simulates chemically reacting low Mach number flows with block-structured adaptive mesh refinement (AMR). The code is built upon the AMReX library, which provides the underlying data structures and tools to manage and operate on them across massively parallel computing architectures. PeleLMeX algorithmic features are inherited from its predecessor PeleLM but key improvements allow representation of more complex physical processes. Together with its compressible flow counterpart PeleC, the thermo-chemistry library PelePhysics and the multi-physics library PeleMP, it forms the Pele suite of open-source reactive flow simulation codes.
97 MATHEMATICS AND COMPUTING↗
An Educational Guide for 2D Stellar Structure Calculations of Rapidly Rotating Stars using the ESTER code
The Evolution STEllaire en Rotation (ESTER) code is the first 2D stellar structure code to be made open-source and freely available to the astronomy and astrophysics community. An important and novel advancement of this code is that it can reproduce the distorted shape and observable signatures (e.g., gravity darkening) of rapidly rotating stars. ESTER also calculates the steady-state large-scale flows within the star, namely their differential rotation and associated meridional circulation. In this report, we explore and document the physics implemented within version 1.1.0rc2 of the ESTER code, in a way that complements published descriptions. We illustrate this physics by plotting how stellar structure parameters vary through stellar interiors at a range of latitudes and at different angular velocities. We investigate how the thin convective envelopes of intermediate mass stars vary with latitude when rapidly rotating, becoming deeper and thicker near the equator. Simple comparisons of ESTER model predictions (e.g., central temperature and density, luminosity) with the output from the Modules for Experiments in Stellar Astrophysics (MESA) code [Paxton et al., 2010] shows generally good agreement. Additional comparisons provide important benchmarking and verification for ESTER as a comparatively young code. Finally, we provide a guide for installing and running the code on our local university cluster, aimed at helping students to begin work.
79 ASTRONOMY AND ASTROPHYSICS↗
Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning
In this work, we present FastConv, a template-based code auto-generation open source library that can automatically generate high-performance deep learning convolution kernels of arbitrary matrices/tensors shapes. FastConv is based on the Winograd algorithm, which is reportedly the highest performing algorithm for the time-consuming convolution layers of convolutional neural networks. ARM CPUs cover a wide range designs and specifications, from embedded devices to HPC-grade CPUs. The leads to the dilemma of how to consistently optimize Winograd-based convolution solvers for convolution layers of different shapes. FastConv addresses this problem by using templates to auto-generate multiple shapes of tuned kernels variants suitable for skinny tall matrices. As a performance portable library, FastConv transparently searches for the best combination of kernel shapes, cache tiles, scheduling of loop orders, packing strategies, access patterns, and online/offline computations. Auto-tuning is used to search the parameter configuration space for the best performance for a given target architecture and problem size. The experiments with layer-wise evaluation on the VGG--16 model confirms a 1.25x performance gains is got by tuning the Winograd library. Integrated comparison results shows 1.02x to 1.40x, 1.14x to 2.17x, and 1.22x and 2.48x speedup is achieved over NNPACK, Arm NN, and FeatherCNN on the Kunpeng 920 beside few cases. Furthermore, problem size performance portability experiments with various convolution shapes shows that FastConv achieves 1.2x to 1.7x speedup and 2x to 22x speedup over NNPACK and ARM NN inference engine using Winograd on Kunpeng 920 . CPU performance portability evaluation on the VGG--16 show an average speedup over NNPACK of 1.42x, 1.21x, 1.26x, 1.37x, 2.26x, and 11.02x is observed on Kunpeng 920, Snapdragon 835, 855, 888, Apple M1, and AWS Graviton2, respectively.
97 MATHEMATICS AND COMPUTING↗
The MolSSI QCArchive project: An open-source platform to compute, organize, and share quantum chemistry data
The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry (QC) results. The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of QC computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface. Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at the website. The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of QC computations for individuals or groups of researchers at any scale. The QCArchiveInfrastructure is open-source (BSD-3C), code repositories can be found at github, and releases can be downloaded via PyPI and Conda. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Data Science > Computer Algorithms and Programming
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A pseudo-two-dimensional (P2D) model for FeS 2 conversion cathode batteries
Conversion cathode materials are gaining interest for secondary batteries due to their high theoretical energy and power density. However, practical application as a secondary battery material is currently limited by practical issues such as poor cyclability. To better understand these materials, we have, for this study, developed a pseudo-two-dimensional model for conversion cathodes. We apply this model to FeS 2 – a material that undergoes intercalation followed by conversion during discharge. The model is derived from the half-cell Doyle–Fuller–Newman model with additional loss terms added to reflect the converted shell resistance as the reaction progresses. We also account for polydisperse active material particles by incorporating a variable active surface area and effective particle radius. Using the model, we show that the leading loss mechanisms for FeS 2 are associated with solid-state diffusion and electrical transport limitations through the converted shell material. The polydisperse simulations are also compared to a monodisperse system, and we show that polydispersity has very little effect on the intercalation behavior yet leads to capacity loss during the conversion reaction. Finally, we provide the code as an open-source Python Battery Mathematical Modeling (PyBaMM) model that can be used to identify performance limitations for other conversion cathode materials.
25 ENERGY STORAGE↗
An automatically curated first-principles database of ferroelectrics
Ferroelectric materials have technological applications in information storage and electronic devices. The ferroelectric polar phase can be controlled with external fields, chemical substitution and size-effects in bulk and ultrathin film form, providing a platform for future technologies and for exploratory research. In this work, we integrate spin-polarized density functional theory (DFT) calculations, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known, previously-proposed, and newly-proposed ferroelectric materials. With our automated workflow, we screen over 67,000 candidate materials from the Materials Project database to generate a dataset of 255 ferroelectric candidates, and propose 126 new ferroelectric materials. We benchmark our results against experimental data and previous first-principles results. The data provided includes atomic structures, output files, and DFT values of band gaps, energies, and the spontaneous polarization for each ferroelectric candidate. Finally, we contribute our workflow and analysis code to the open-source python packages atomate and pymatgen so others can conduct analogous symmetry driven searches for ferroelectrics and related phenomena.
36 MATERIALS SCIENCE↗
Development of an open-source segmented blade design tool
As wind turbines continue to grow ever larger to reduce the cost of energy, their blades follow suit, with the largest commercial offshore blades extending past 100 m. Massive blades such as these raise key transportation and manufacturing challenges, especially for land-based turbines. Segmented blades are one solution and are garnering increased industry and research interest. In this work, a detailed mechanical joint model is integrated into the Wind-Plant Integrated System Design and Engineering Model (WISDEM ® ), which will facilitate future segmented blade research and optimization. WISDEM is used to design a wind turbine with 100-m segmented blades. This wind turbine design is compared to other machines with 100-m monolithic blades designed for rail-transportability. The designs are compared in terms of blade mass and cost, turbine capital cost, annual energy production, and levelized cost of energy, with monolithic designs being the lightest and most economical. However, this result may vary by wind plant location. A variety of segmentation joint types exist, and they will inevitably vary in parameters such as cost, spanwise location, and physical characteristics. This work examines the sensitivity of wind turbine design drivers and annual energy production to a variety of the aforementioned parameters, using the open-source wind turbine design codes OpenFAST and WISDEM, finding that joint mass, stiffness, and location can have significant effects on design drivers.
17 WIND ENERGY↗
Towards exascale for wind energy simulations
We examine large-eddy-simulation modeling approaches and computational performance of two open-source computational fluid dynamics codes for the simulation of atmospheric boundary layer flows that are of direct relevance to wind energy production. The first code, NekRS, is a high-order, unstructured-grid, spectral element code. The second code, AMR-Wind, is a second-order, block-structured, finite-volume code with adaptive mesh refinement capabilities. The objective of this study is to co-develop these codes in order to improve model fidelity and performance for each. These features will be critical for running ABL-based applications such as wind farm analysis on advanced computing architectures. To this end, we investigate the performance of NekRS and AMR-Wind on the Oak Ridge Leadership Facility supercomputers Summit, using 4 to 800 nodes (24 to 4,800 NVIDIA V100 GPUs), and Crusher, the testbed for the Frontier exascale system, using 18 to 384 Graphics Compute Dies on AMD MI250X GPUs. We compare strong- and weak-scaling capabilities, linear solver performance, and time to solution. We also identify leading inhibitors to parallel scaling.
17 WIND ENERGY↗
Developing an Automated Uncertainty Quantification Tool to Improve Watershed-Scale Predictions of Water and Nutrient Cycling
Managing the flow of water, nutrients, and contaminants in watersheds is vital to addressing pressing issues related to water scarcity, access to clean drinking water, energy production, resilience to natural and anthropogenic perturbations, and ecological restoration. Decisions about the management of watersheds critically depend on the accuracy with which the flow of water and chemicals through the watershed can be predicted by computer models. Prediction uncertainty can be reduced by matching the model to data, which are collected in the field at great expense. The contribution of watershed characterization data to reducing uncertainty of relevant model predictions can be evaluated in a so-called data-worth analysis, which provides transparent, quantitative metrics about a data set’s value for the support of relevant watershed management objectives. To achieve this goal, we developed a software package that implements the data-worth analysis approach for use with state-of-the-art watershed models. The purpose of the proposed data-worth analysis is to help decision-makers allocate resources for watershed characterization such that the uncertainty in model predictions can be significantly reduced, which leads to better, more effective management decisions. At the same time, watershed characterization costs can be reduced. The specific technical objectives of this SBIR/STTR Phase II project were to develop a framework and associated software toolsets that implement the uncertainty quantification and data-worth analysis approach for use with state-of-the-art watershed models. This goal was achieved by (A) developing a user-friendly, robust software package that is accessible to a wide audience, including watershed managers, policy-makers, and public stakeholders; (B) by demonstrating application of the prototype on several use cases that are representative of complex watershed management challenges spanning a range of scales and that consider different open-source, DOE-based codes and other modeling platforms; and (C) by gathering information about the needs and requirements from potential users to help guide future developments, ensuring that the final product will be commercially viable. The developed software consists of a graphical user interface that guides the user through a sequence of analysis steps, supported by toolsets that leverage state-of-the-art computational simulation-optimization capabilities. A prototype of the software runs on multiple platforms (PC, Mac, multi-processor Linux environment), is linked to diverse watershed simulators (e.g., ECOSYS, TOUGH2, TOUGHREACT, Amanzi-ATS), performs multiple analysis tasks (predictive simulations, sensitivity analysis, uncertainty analysis, automatic parameter estimation, and data-worth analysis, multicomponent geothermometry), and is readily extensible to include external simulators and analysis tools. The software is being commercialized and will be continually updated to address user needs.
58 GEOSCIENCES↗
Seascape Interface Control Document
This paper serves as the Interface Control Document (ICD) for the Seascape automated test harness developed at Sandia National Laboratories. The primary purposes of the Seascape system are: (1) provide a place for accruing large, curated, labeled data sets useful for developing and evaluating detection and classification algorithms (including, but not limited to, supervised machine learning applications) (2) provide an automated structure for specifying, running and generating reports on algorithm performance. Seascape uses GitLab, Nexus, Solr, and Banana, open source software, together with code written in the Python language, to automatically provision and configure computational nodes, queue up jobs to accomplish algorithms test runs against the stored data sets, gather the results and generate reports which are then stored in the Nexus artifact server.
97 MATHEMATICS AND COMPUTING↗
Development of MHD for NekRS
A spectral-element-based formulation of incompressible MHD is presented in the context of the open-source fluid-thermal code, Nek5000/RS. The formulation supports magnetic fields in a solid domain that surrounds the fluid domain. Several steady-state and time-transient model problems are presented as part of the code verification process. Nek5000/RS is designed for large-scale turbulence simulations, which will be the next step with this new MHD capability.
97 MATHEMATICS AND COMPUTING↗
Nek5000/RS performance on advanced GPU architectures
The authors explore performance scalability of the open-source thermal-fluids code, NekRS, on the U.S. Department of Energy's leadership computers, Crusher, Frontier, Summit, Perlmutter, and Polaris. Particular attention is given to analyzing performance and time-to-solution at the strong-scale limit for a target efficiency of 80%, which is typical for production runs on the DOE's high-performance computing systems. Several examples of anomalous behavior are also discussed and analyzed.
97 MATHEMATICS AND COMPUTING↗
ACDC (Automated Campbell Diagram Code) [SWR-26-042]
This application provides a web-based graphical user interface to generating Campbell Diagrams and visualizing mode shapes for OpenFAST turbine models. Determining the aeroelastic stability and dynamic characteristics of wind turbines is a critical step in turbine design and analysis. Historically, extracting natural frequencies and mode shapes from OpenFAST—the industry-standard whole-turbine simulation code—has been a fragmented and tedious process. It required manual model configuration, command-line linearization execution, and complex post-processing via proprietary scripts to handle rotating-frame dynamics. To address these workflow bottlenecks, we present the Automated Campbell Diagram Code (ACDC), an open-source graphical software tool developed by the National Laboratory of the Rockies (NLR) under the DOE-funded Distributed Wind Aeroelastic Modeling (dWAM) project. ACDC streamlines the end-to-end linearization and stability analysis workflow into a single, intuitive cross-platform application. The software guides users through OpenFAST model configuration, definition of operating points, and the automated execution of steady-state trim and linearization simulations. Under the hood, ACDC automates the complex mathematical post-processing steps required for rotating systems, including Multi-Blade Coordinate (MBC) transformations, eigenanalysis, and advanced modal tracking utilizing the Modal Assurance Criterion (MAC) and spectral clustering. Finally, ACDC processes these results to automatically generate Campbell diagrams and features a robust 3D visualization engine to animate full-system mode shapes. By eliminating the reliance on external post-processing environments and manual data manipulation, ACDC significantly accelerates dynamic analysis and lowers the barrier to entry for wind energy researchers and engineers.
Summerville, Brent [National Laboratory of the Roc↗
Tiered Energy Use in Buildings (TEB)
This tool creates a set of building energy simulations and organizes them according to a tier-based model representing circuits that will be on or off depending on a microgrid controller (not included in this software). This Python based code uses the open-source RCBuildingSimulator that is under an amended MIT license. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-2528 O
Villa, Daniel↗
Entity—Hardware-agnostic Particle-in-cell Code for Plasma Astrophysics. I. Curvilinear Special Relativistic Module
Entity is a new-generation, fully open-source particle-in-cell (PIC) code developed to overcome key limitations in astrophysical plasma modeling, particularly the extreme separation of scales and the performance challenges associated with evolving, GPU-centric computing infrastructures. It achieves hardware-agnostic performance portability across various GPU and CPU architectures using the Kokkos library. Crucially, Entity maintains a high standard for usability, clarity, and customizability, offering a robust and easy-to-use framework for developing new algorithms and grid geometries, which allows extensive control without requiring edits to the core source code. This paper details the core general-coordinate special relativistic module. Entity is the first PIC code designed to solve the Vlasov–Maxwell system in general coordinates, enabling a coordinate-agnostic framework that provides the foundational structure for straightforward extension to arbitrary coordinate geometries. The core methodology achieves numerical stability by solving particle equations of motion in the global orthonormal Cartesian basis, despite using generalized coordinates like Cartesian, axisymmetric spherical, and quasi-spherical grids. Charge conservation is ensured via a specialized current deposition technique using conformal currents. The code exhibits robust scalability and performance portability on major GPU platforms (AMD MI250X, NVIDIA A100, and Intel Max Series), with the 3D particle pusher and the current deposition operating efficiently at about 2 ns per particle per time step. Functionality is validated through a comprehensive suite of standard Cartesian plasma tests and the accurate modeling of relativistic magnetospheres in curvilinear axisymmetric geometries.
Hakobyan, Hayk [Flatiron Institute, New York, NY (↗
Code for the manuscript "Mori-Zwanzig Modal Decomposition"
We would like to create an open source repository in LANL's github on code written in Julia, in which we implement and extend the data-driven Mori-Zwanzig method for extracting large-scale spatio-temporal structures from data, which we call MZMD. This method is an extension of Dynamic Mode Decomposition (DMD) in which Mori-Zwanzig memory kernels are included into the associated companion matrix. In the code we would like to release, we apply MZMD to a flow over a cylinder with Reynolds number 100 rather than the much larger data set used in the associated manuscript. DMD is used extensively in the fluid dynamics community mainly for extracting large scale spatio-temporal structures (patters) from flow data. This is useful for understanding the key mechanisms that generate certain complex dynamical process relevant in engineering design. In MZMD, we improve upon DMD by adding the Mori-Zwanzig memory kernels, and show this improvement is especially important in strongly nonlinear regions of the flow.
Woodward, Michael↗
Logical error rates for the surface code under a mixed coherent and stochastic circuit-level noise model inspired by trapped ions
With fault-tolerant quantum computing (FTQC) on the horizon, it is critical to understand sources of logical errors in plausible hardware implementations of quantum error-correcting codes. Detailed error modeling of computational instructions on particular FTQC architectures will enable the better prediction of error propagation in FT-encoded quantum circuits while revealing where greater attention is needed in hardware design. In this work, we consider logical error rates for the surface code implemented on a hypothetical grid-based trapped-ion quantum charge-coupled device architecture. Specifically, we construct logical channels for the idling surface code and examine its diamond error under a mixed coherent and stochastic circuit-level noise model inspired by trapped ions. We include the coherent dephasing noise that is known to accumulate during physical qubit idling and transport in these systems, determining idling and transport durations using the time-resolved output of an open-source trapped-ion surface code compiler. To estimate expectation values of logical Pauli observables following hardware circuits containing non-Clifford sources of noise, we utilize a Monte Carlo technique to sample from an underlying quasiprobability distribution of Clifford circuits that we independently simulate in a phase-sensitive fashion. We verify error suppression up to code distance 𝑑 = 11 at coherent dephasing rates near and below those of current-generation trapped-ion quantum computers and find that logical error rates align with those of analogous fully stochastic simulations in this regime. Exploring higher dephasing rates at 𝑑 = 3−5, we find evidence for growing coherent rotations about all three logical Pauli axes, increased diagonal logical error process matrix elements relative to those of stochastic simulations, and a reduced dephasing rate threshold. Overall, our work paves a way toward realistic hardware emulation of small fault-tolerant quantum processes, e.g., members of an FTQC instruction set.
Quantum benchmarking↗