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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Aimsgb: An algorithm and open-source python library to generate periodic grain boundary structures

An algorithm implemented in an open-source python library was developed for building periodic grain boundary models in a universal fashion. The software framework, aimsgb, aims to generate tilt and twist grain boundaries from an input cubic or non-cubic crystal structure for ab-initio and classical atomistic simulation. It can output a coincidence site lattice (CSL) grain boundary for a cubic input structure and a non-CSL grain boundary for a non-cubic input structure. This framework has two useful features: (i) it can calculate all the CSL matrices for generating CSL from a given Sigma (Σ) value and rotation axis, allowing the users to build the specific CSL and grain boundary models; (ii) it provides a convenient command line tool to enable high-throughput generation of tilt and twist grain boundaries by assigning an input crystal structure, Σ value, rotation axis, and grain boundary plane. Here, the developed algorithm in the open-source python library is expected to facilitate studies of grain boundary in materials science. The software framework is available on the website: aimsgb.org.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Enriched immersed finite element and isogeometric analysis: algorithms and data structures

Immersed finite element methods provide a convenient analysis framework for problems involving geometrically complex domains, such as those found in topology optimization and microstructures for engineered materials. However, their implementation remains a major challenge due to, among other things, the need to apply nontrivial stabilization schemes and generate custom quadrature rules. This article introduces the robust and computationally efficient algorithms and data structures comprising an immersed finite element preprocessing framework. The input to the preprocessor consists of a background mesh and one or more geometries defined on its domain. The output is structured into groups of elements with custom quadrature rules formatted such that common finite element assembly routines may be used without or with only minimal modifications. The key to the preprocessing framework is the construction of material topology information, concurrently with the generation of a quadrature rule, which is then used to perform enrichment and generate stabilization rules. While the algorithmic framework applies to a wide range of immersed finite element methods using different types of meshes, integration, and stabilization schemes, the preprocessor is presented within the context of the extended isogeometric analysis. This method utilizes a structured B-spline mesh, a generalized Heaviside enrichment strategy considering the material layout within individual basis functions’ supports, and face-oriented ghost stabilization. Using a set of examples, the effectiveness of the enrichment and stabilization strategies is demonstrated alongside the preprocessor’s robustness in geometric edge cases. Additionally, the performance and parallel scalability of the implementation are evaluated.

Computer implementation↗
DOE OSTI2025

Algorithms and file structures to extend and enhance liquid chromatography and ion mobility mass spectrometry workflows (CRADA Final Report)

The purpose of this project was to continue supporting customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based protein and metabolite characterization. PNNL worked with Agilent to design, implement, evaluate, and demonstrate new algorithms and integrated them as functionalities into the PNNL-PreProcessor software. The project augmented PNNL’s capabilities to analyze complex proteomics and metabolomics samples. These capabilities are directly beneficial to DOE and PNNL efforts to characterize and analyze these compounds in microbial and plant communities. The project assisted Agilent in further developing improved instrument-software solutions combining liquid chromatography and ion mobility with mass spectrometry for widespread applications in life sciences and other fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The XtalOpt Evolutionary Algorithm for Crystal Structure Prediction

Significant progress has been made in the field of a priori crystal structure prediction, with a number of recent remarkable success stories. Herein, we briefly outline the methods that have been developed for finding the global minimum structure and interesting local minima without the need for experimental information. Focus is placed on describing the XTALOPT evolutionary algorithm (EA) developed in our group towards this end. XTALOPT is published under well-known open-source licenses, and the EA searches can be analyzed via the AVOGADRO chemical editor and visualizer. We describe new algorithmic developments that have made it possible to predict the structures of ever-more complex crystalline lattices. Benchmark tests, which clearly illustrate how the new developments improve the success rate and accelerate the discovery of the global minimum structure, are carried out. Lastly, we describe how XTALOPT has been employed to predict novel ternary hydrides that have the propensity for high-temperature superconductivity under pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Advanced fuel fusion, phase space engineering, and structure-preserving geometric algorithms

Non-thermal advanced fuel fusion trades the requirement of a large amount of recirculating tritium in the system for that of large recirculating power. Phase space engineering technologies utilizing externally injected electromagnetic fields can be applied to meet the challenge of maintaining non-thermal particle distributions at a reasonable cost. The physical processes of the phase space engineering are studied from a theoretical and algorithmic perspective. It is emphasized that the operational space of phase space engineering is limited by the underpinning symplectic dynamics of charged particles. The phase space incompressibility according to the Liouville theorem is just one of many constraints, and Gromov's non-squeezing theorem determines the minimum footprint of the charged particles on every conjugate phase space plane. In this sense and level of sophistication, the mathematical abstraction of phase space engineering is symplectic topology. To simulate the processes of phase space engineering, such as the Maxwell demon and electromagnetic energy extraction, and to accurately calculate the minimum footprints of charged particles, recently developed structure-preserving geometric algorithms can be used. The family of algorithms conserves exactly, on discretized spacetime, symplecticity and thus incompressibility, non-squeezability, and symplectic capacities. The algorithms apply to the dynamics of charged particles under the influence of external electromagnetic fields as well as the charged particle–electromagnetic field system governed by the Vlasov–Maxwell equations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Block2 : A comprehensive open source framework to develop and apply state-of-the-art DMRG algorithms in electronic structure and beyond

block2 is an open source framework to implement and perform density matrix renormalization group and matrix product state algorithms. Out-of-the-box it supports the eigenstate, time-dependent, response, and finite-temperature algorithms. In addition, it carries special optimizations for ab initio electronic structure Hamiltonians and implements many quantum chemistry extensions to the density matrix renormalization group, such as dynamical correlation theories. The code is designed with an emphasis on flexibility, extensibility, and efficiency and to support integration with external numerical packages. Here, we explain the design principles and currently supported features and present numerical examples in a range of applications.

Chemistry↗
DOE OSTI2021

Algorithms and file structures to enhance software workflows for ion mobility mass spectrometry (IM-MS): CRADA 410 (Final Report)

This document is the final report for CRADA 410 (Project No. 72496). The purpose of this project was supporting customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based metabolite characterization. PNNL worked with Agilent to evaluate and improve the integration of ion mobility into existing MS data analysis methods of Agilent software tools. The project augmented PNNL’s capabilities to analyze complex omics samples. These capabilities are directly beneficial to DOE and PNNL efforts to characterize and analyze compounds in microbial and plant communities. The project assisted Agilent in further developing improved instrument-software solutions combining ion mobility with mass spectrometry for widespread applications in life sciences and other fields.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

SU-E-T-81: Comparison of Microdosimetric Quantities Calculated Using the Track Structure Monte Carlo Algorithms Geant4-DNA and NOREC

Purpose: Microdosimetric quantities, such as the lineal energy, have been shown to correlate with the biological response to radiation and the relative biological effect of different radiation types. Track-structure Monte Carlo simulations are an important tool for investigating these responses and for developing mechanistic models to explain them. However, some of the cross-sectional data used in these algorithms has large uncertainties; thus, it is important to investigate how the implementation of the different codes affects the quantities of interest. Methods: Two of the most widely-used publicly available track-structure Monte Carlo codes, Geant4-DNA and NOREC, were used generate electron tracks for two particle sources. One source was a mono-energetic parallel beam of electrons with energies from 5 to 500-keV, and the lineal energy for each track was calculated in 1-mm-spheres arranged in planar arrays at multiple distances from the source. The second source was mono-energetic, uniformly-distributed, and isotropic source, and the lineal energy was scored in a single 30-mm-sphere for energies between 300-eV and 5-keV. Results: The dose-mean lineal energy for the parallel-beam simulations almost all agreed within 5%. For the uniformly-distributed source, at the lowest energies there was strong agreement between the algorithms, but the Geant4-DNA simulations showed slightly more high-energy events for more energetic electrons, but the dose-mean lineal energy agreed to within 4% for all energies. Conclusion: While there were slight differences in the results between the codes, these were consistent with previous studies of the stopping power and angular scattering distributions. Importantly, the computation time for Geant4-DNA was larger than for NOREC, largely due to approximations used in the NOREC for energies below 10-eV. This study shows that these approximation does not have a major impact on the microdosimetry on the energy and length scales investigated.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

An Efficient Algorithm for Automatic Structure Optimization in X-ray Standing-Wave Experiments

We present that x-ray standing-wave photoemission experiments involving multilayered samples are emerging as unique probes of the buried interfaces that are ubiquitous in current device and materials research. Such data require for their analysis a structure optimization process comparing experiment to theory that is not straightforward. In this work, we present a new computer program for optimizing the analysis of standing-wave data, called SWOPT, that automates this trial-and-error optimization process. The program includes an algorithm that has been developed for computationally expensive problems: so-called black-box simulation optimizations. It also includes a more efficient version of the Yang X-ray Optics Program (YXRO) [Yang, S.-H., Gray, A.X., Kaiser, A.M., Mun, B.S., Sell, B.C., Kortright, J.B., Fadley, C.S., J. Appl. Phys. 113, 1 (2013)] which is about an order of magnitude faster than the original version. Human interaction is not required during optimization. We tested our optimization algorithm on real and hypothetical problems and show that it finds better solutions significantly faster than a random search approach. The total optimization time ranges, depending on the sample structure, from minutes to a few hours on a modern laptop computer, and can be up to 100x faster than a corresponding manual optimization. Finally, these speeds make the SWOPT program a valuable tool for realtime analyses of data during synchrotron experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Calculating the grain boundary inclination of voxelated grain structures using a smoothing algorithm

We have developed a flexible method for calculating the grain boundary (GB) inclinations of voxelated grain structure data using smoothing algorithms. We compared the performance of four algorithms: the linear interpolation, Allen–Cahn, level-set, and vertex algorithms. We assessed their accuracy using 2D and 3D cases with known inclinations. The vertex algorithm provided the best balance between accuracy and efficiency for 2D structures while the linear interpolation algorithm provided the best balance for 3D structures. We compared the GB inclinations calculated using our smoothing method on a 3D high energy X-ray diffraction microscopy (HEDM) dataset to those determined by meshing the GBs. The two approaches determined similar GB plane distributions, though they varied significantly at triple junctions. In conclusion, the smoothing method was demonstrated for two sources of 3D voxelated grain structures: HEDM data and results from Monte Carlo Potts grain growth simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Genetic algorithm prediction of crystal structure of metastable Si-IX phase

We performed genetic algorithm search for the atomic structure of the long Lime unsolved Si-IX phase. We found two new structures with space groups of P4(2)/m and P-4, respectively, which have lattice parameters in excellent agreement with the experimental data. The phonon calculations showed that the P4(2)/m structure exhibits a soft phonon mode, while the P-4 structure is dynamically stable. Our calculation also showed that the P-4 structure is a meta-stable structure in a pressure range from 0 to 40 GPa, The Si-IX phase could be a mixed phase consisting of the P4(2)/m and the P-4 structures. Published by Elsevier Ltd.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Pele: An Exascale-Ready Suite of Combustion Codes

High fidelity simulations of realistic combustion devices are extremely demanding computationally because of the requirements to capture complex fuel chemical decomposition, its intricate interactions with turbulent, often multiphase, flows, and the wide separation of space and time scales between the thin flame and the device boundaries. Software required to carry out such computations tends to be extremely complex, particularly when designed to exploit hardware accelerators, and can be difficult to port and maintain. We present Pele, a performance portable suite of tools for the simulation of combustion systems, including codes to evolve reactive multiphase configurations in the low Mach number and compressible flow regimes, along with a set of inter-compatible post processing and in situ analysis tools. The Pele suite of tools is built on top of the AMReX framework for block-structured adaptive mesh refinement, which provides efficient data structures and algorithms that enable the development of a wide variety of efficient mesh and particle based PDE integration schemes. A hierarchical MPI+X parallelism scheme supports CPU-only and accelerated architectures, where X can be OpenMP, CUDA, and HIP based approaches for intra-node computational work distribution. The algorithms and data structures underlying the Pele simulation and analysis tools are highly scalable and performant across a wide variety of high-performance computing platforms, including DOEs newest exascale-class machines, Frontier and Aurora. The simulation and analysis tools are fully documented and freely distributed as open source via GitHub. We present key algorithmic and software challenges, solution strategies, performance and resulting set of capabilities.

AMReX↗