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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A quasi-static particle-in-cell algorithm based on an azimuthal Fourier decomposition for highly efficient simulations of plasma-based acceleration: QPAD

The three-dimensional (3D) quasi-static particle-in-cell (PIC) algorithm is a very efficient method for modeling short-pulse laser or relativistic charged particle beam–plasma interactions. In this algorithm, the plasma response, i.e., plasma wave wake, to a non-evolving laser or particle beam is calculated using a set of Maxwell’s equations based on the quasi-static approximate equations that exclude radiation. The plasma fields are then used to advance the laser or beam forward using a large time step. The algorithm is many orders of magnitude faster than a 3D fully explicit relativistic electromagnetic PIC algorithm. It has been shown to be capable to accurately model the evolution of lasers and particle beams in a variety of scenarios. Additionally, at the same time, an algorithm in which the fields, currents and Maxwell equations are decomposed into azimuthal harmonics has been shown to reduce the algorithmic complexity of a 3D explicit PIC algorithm to that of a 2D algorithm when the expansion is truncated while maintaining accuracy for problems with near azimuthal symmetry. This hybrid algorithm uses a PIC description in r–z and a gridless description in . We describe a novel method that combines the quasi-static and hybrid PIC methods. This algorithm expands the fields, charge and current density into azimuthal harmonics. A set of the quasi-static field equations is derived for each harmonic. The complex amplitudes of the fields are then solved using the finite difference method. The beam and plasma particles are advanced in Cartesian coordinates using the total fields. Details on how this algorithm was implemented using a similar workflow to an existing quasi-static code, QuickPIC, are presented. The new code is called QPAD for QuickPIC with Azimuthal Decomposition. Benchmarks and comparisons between a fully 3D explicit PIC code (OSIRIS), a full 3D quasi-static code (QuickPIC), and the new quasi-static PIC code with azimuthal decomposition (QPAD) are also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗
DOE OSTI2024

E(n)-Equivariant cartesian tensor message passing interatomic potential

Machine learning potential (MLP) has been a popular topic in recent years for its capability to replace expensive first-principles calculations in some large systems. Meanwhile, message passing networks have gained significant attention due to their remarkable accuracy, and a wave of message passing networks based on Cartesian coordinates has emerged. However, the information of the node in these models is usually limited to scalars, and vectors. In this work, we propose High-order Tensor message Passing interatomic Potential (HotPP), an E(n) equivariant message passing neural network that extends the node embedding and message to an arbitrary order tensor. By performing some basic equivariant operations, high order tensors can be coupled very simply and thus the model can make direct predictions of high-order tensors such as dipole moments and polarizabilities without any modifications. The tests in several datasets show that HotPP not only achieves high accuracy in predicting target properties, but also successfully performs tasks such as calculating phonon spectra, infrared spectra, and Raman spectra, demonstrating its potential as a tool for future research.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

Abstract In this work, we expand on a dataset recently introduced for protein interface prediction (PIP), the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset of 42,112 complexes for machine learning of protein interfaces. While the original DIPS dataset contains only the Cartesian coordinates for atoms contained in the protein complex along with their types, DIPS-Plus contains multiple residue-level features including surface proximities, half-sphere amino acid compositions, and new profile hidden Markov model (HMM)-based sequence features for each amino acid, providing researchers a curated feature bank for training protein interface prediction methods. We demonstrate through rigorous benchmarks that training an existing state-of-the-art (SOTA) model for PIP on DIPS-Plus yields new SOTA results, surpassing the performance of some of the latest models trained on residue-level and atom-level encodings of protein complexes to date.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Anisotropic E × B shearing rate in a magnetic island

We derive the E × B shearing rate associated with vortex flow inside a macroscopic magnetic island (MI) in axisymmetric toroidal geometry. Due to the elongation of the MI and incompressibility of the E × B flow, the shearing rate near X-points is much lower than that near the mid-plane (x-axis of the local Cartesian coordinate) of the MI on the same flux surface. Furthermore, the rate formally vanishes at the X-points where the local poloidal magnetic field associated with the MI stagnates. Here, this calculation of E × B shearing profile and, in particular, minimal E × B shear near the X-points is consistent with the recent experimental finding that turbulence tends to spread into an MI through regions around the X-points and can contribute to more thorough quantitative interpretation of the results from experiments and simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Accurate prediction of global-density-dependent range-separation parameters based on machine learning

In this work, we develop an accurate and efficient XGBoost machine learning model for predicting the global-density-dependent range-separation parameter, ωGDD, for long-range corrected functional (LRC)-ωPBE. This ωGDDML model has been built using a wide range of systems (11 466 complexes, ten different elements, and up to 139 heavy atoms) with fingerprints for the local atomic environment and histograms of distances for the long-range atomic correlation for mapping the quantum mechanical range-separation values. The promising performance on the testing set with 7046 complexes shows a mean absolute error of 0.001 117 a0−1 and only five systems (0.07%) with an absolute error larger than 0.01 a0−1, which indicates the good transferability of our ωGDDML model. In addition, the only required input to obtain ωGDDML is the Cartesian coordinates without electronic structure calculations, thereby enabling rapid predictions. LRC-ωPBE(ωGDDML) is used to predict polarizabilities for a series of oligomers, where polarizabilities are sensitive to the asymptotic density decay and are crucial in a variety of applications, including the calculations of dispersion corrections and refractive index, and surpasses the performance of all other popular density functionals except for the non-tuned LRC-ωPBE. Finally, LRC-ωPBE (ωGDDML) combined with (extended) symmetry-adapted perturbation theory is used in calculating noncovalent interactions to further show that the traditional ab initio system-specific tuning procedure can be bypassed. The present study not only provides an accurate and efficient way to determine the range-separation parameter for LRC-ωPBE but also shows the synergistic benefits of fusing the power of physically inspired density functional LRC-ωPBE and the data-driven ωGDDML model.

Chemistry↗
DOE OSTI2026

SHarmonic: A fast and accurate implementation of spherical harmonics for electronic-structure calculations

The authors present SHarmonic, a new implementation of the spherical harmonics targeted for electronic-structure calculations. Their approach is to use explicit formulas for the harmonics written in terms of normalized Cartesian coordinates. This approach results in a code that is as precise as other implementations while being at least one order of magnitude more computationally efficient. The library can run on graphics processing units as well, achieving an additional order of magnitude in execution speed. This new implementation is simple to use and is provided under an open-source license; it can be readily used by other codes to avoid the error-prone and cumbersome implementation of the spherical harmonics.

Mathematics and Computing↗
DOE OSTI2022

Handing off the outcome of binary neutron star mergers for accurate and long-term postmerger simulations

In this work, we perform binary neutron star (BNS) merger simulations in full dynamical general relativity with IllinoisGRMHD, on a Cartesian grid with adaptive-mesh refinement. After the remnant black hole has become nearly stationary, the evolution of the surrounding accretion disk on Cartesian grids over long timescales (~1s) is suboptimal, as Cartesian coordinates over-resolve the angular coordinates at large distances, and the accreting plasma flows obliquely across coordinate lines dissipating angular momentum artificially from the disk. To address this, we present the HandOff, a set of computational tools that enables the transfer of general relativistic magnetohydrodynamic (GRMHD) and spacetime data from IllinoisGRMHD to harm3d, a GRMHD code that specializes in modeling black hole accretion disks in static spacetimes over long timescales, making use of general coordinate systems with spherical topology. We demonstrate that the handoff allows for a smooth and reliable transition of GRMHD fields and spacetime data, enabling us to efficiently and reliably evolve BNS dynamics well beyond merger. We also discuss future plans, which involve incorporating advanced equations of state and neutrino physics into BNS simulations using the HandOff approach.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Symbolic pregression: Discovering physical laws from distorted video

In this work, we present a method for unsupervised learning of equations of motion for objects in raw and optionally distorted unlabeled synthetic video (or, more generally, for discovering and modeling predictable features in time-series data). We first train an autoencoder that maps each video frame into a low-dimensional latent space where the laws of motion are as simple as possible, by minimizing a combination of nonlinearity, acceleration, and prediction error. Differential equations describing the motion are then discovered using Pareto-optimal symbolic regression. We find that our pre-regression (“pregression”) step is able to rediscover Cartesian coordinates of unlabeled moving objects even when the video is distorted by a generalized lens. Using intuition from multidimensional knot theory, we find that the pregression step is facilitated by first adding extra latent space dimensions to avoid topological problems during training and then removing these extra dimensions via principal component analysis. An inertial frame is autodiscovered by minimizing the combined equation complexity for multiple experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Theoretical Assessment of the Transition Between Electron Emission Mechanisms for Nonplanar Diodes

Theoretically and computationally describing the operation of nanodiodes requires characterizing the transitions between multiple electron emission mechanisms for nanodiodes with complicated geometries. This motivates our development of techniques to determine when simplified theories for individual mechanisms suffice compared to more complete, but more computationally expensive, models. Leveraging recent theories that define a canonical gap distance to translate planar theory to nonplanar diodes, we derive the conditions for the transitions among thermal emission, field emission, and space-charge-limited current density (SCLCD) in vacuum and with collisions for non-Cartesian coordinate systems, including spherical, cylindrical, and prolate spheroidal coordinate systems. Particle-in-cell (PIC) simulations of the current density as a function of applied voltage for a tip-to-plate geometry in vacuum agreed qualitatively with the asymptotes for thermal emission at low voltage and SCLCD at higher voltage using the canonical gap distance. As a result, this demonstrates the utility of this approach for guiding system design and suggests future extensions to save simulation time for more realistic geometries that are more computationally expensive.

Conformal mapping↗
DOE OSTI2021

AEVmod – Atomic Environment Vector Module Documentation

This report outlines the mathematical formulation for the atomic environment vector (AEV) construction used in the aevmod software package. The AEV provides a summary of the geometry of a molecule or atomic configuration. We also present the formulation for the analytical Jacobian of the AEV with respect to the atomic Cartesian coordinates. The software provides functionality for both the AEV and AEV-Jacobian, as well as the AEV-Hessian which is available via reliance on the third party library Sacado.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Study of Quadrupole Fringe Fields in the Interaction Region of the Hadron Storage Ring of the Electron Ion Collider

Fringe fields in quadrupole magnets are usually neglected in studies of beam dynamics at accelerators. However, the extreme optical parameters present in the final focus of a collider such as the Electron–Ion Collider (EIC) may give rise to effects that should not be overlooked. The calculation of quadrupole fringe fields presented in this study follows the procedure outlined in Ref. [1], specialized to the case of a straight reference orbit (i.e., with no dipole field component). A right-handed Cartesian coordinate system is employed, with the $z$-axis aligned with the quadrupole axis and $x$ and $y$ denoting the horizontal and vertical transverse coordinates, respectively. The magnetic quadrupole field gradient, $G = \partial B_y / \partial x$, transitions from its peak value inside the quadrupole—where it is nearly independent of the longitudinal coordinate $z$—to zero at some distance beyond the magnet edge. Consequently, $G$ is treated as a function of $z$. The region over which this variation occurs is defined as the quadrupole fringe field region. The study begins with the development of a description of the magnetic field in the fringe region using a power-series expansion in the transverse coordinates $x$and $y$, consistent with the longitudinally varying gradient. A model for the $z$-dependence of the gradient is then proposed and adjusted to reproduce magnetic field data obtained from three-dimensional field calculations. To evaluate the impact of the fringe fields on beam dynamics, the corresponding vector potential is derived and incorporated into a Hamiltonian formulation of particle motion. The significance of the fringe fields is quantified by calculating the amplitude-dependent tune shift from the Hamiltonian. Using linear beam optics parameters of the Hadron Storage Ring (HSR) of the EIC, the tune shift due to the fringe fields of all quadrupole magnets in the IR-6 interaction region is evaluated. Finally, the resulting tune shifts are compared with those arising from other nonlinear field components present in the HSR.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Introduction to Special Relativity

The goal of this lecture is to introduce the student to the theory of Special Relativity. Not to overload the content with mathematics, the author will stick to the simplest cases; in particular only reference frames using Cartesian coordinates and translating along the common x-axis as in Fig. 1 will be used. The general expressions will be quoted or may be found in the cited literature.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Systems Level Fuel Cycle Modeling in TMAP8 - A Demonstration

The tritium migration analysis program (TMAP) has been used for tritium inventory tracking and analysis for several years, and the Multiphysics Object Oriented Simulation Environment (MOOSE)-based TMAP8 has several improvements over TMAP4 and TMAP7, such as support for multiple dimensions and non-cartesian coordinate systems, as well as interoperability with sub-apps at higher and lower length scales. We demonstrate that TMAP8 has the additional capacity to solve systems-level problems using zero-dimensional ordinary differential equations by reproducing a literature model which describes a systems-level fuel-cycle of tritium inventory in a hypothetical fusion power plant. The capacity to run several coupled multi-scale physics calculations as part of a single package will be necessary for accurate blanket and fuel-cycle design.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Parallel transport sweeps on two-dimensional cartesian and hexagonal grids

This paper aims to provide a proof of concept for parallel transport sweeps on two-dimensional hexagonal grids for the discrete ordinates transport equation. While the method is an extension of the popular and well-established Koch-Baker-Alcoulffe (KBA) algorithm, there are significant differences between the cartesian and hexagonal grid and thereafter sweep. The most important is the three-way connectivity of hexagons within the grid which creates greater dependencies between the elements. The KBA method in structured orthogonal grids was first implemented in the DRAGON5 code and the method is first described here. The differences in implementation for the hexagonal grid are also described. Benchmark results are also presented, showing roughly 10 times speedup in computational times with roughly 100 processors, in both cases. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

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 (↗
DOE OSTI2021

Computational general relativistic force-free electrodynamics: I. Multi-coordinate implementation and testing

General relativistic force-free electrodynamics is one possible plasma-limit employed to analyze energetic outflows in which strong magnetic fields are dominant over all inertial phenomena. The amazing images of black hole (BH) shadows from the Galactic Center and the M87 galaxy provide a first direct glimpse into the physics of accretion flows in the most extreme environments of the universe. The efficient extraction of energy in the form of collimated outflows or jets from a rotating BH is directly linked to the topology of the surrounding magnetic field. We aim at providing a tool to numerically model the dynamics of such fields in magnetospheres around compact objects, such as BHs and neutron stars. To do so, we probe their role in the formation of high energy phenomena such as magnetar flares and the highly variable teraelectronvolt emission of some active galactic nuclei. In this work, we present numerical strategies capable of modeling fully dynamical force-free magnetospheres of compact astrophysical objects. Here, we provide implementation details and extensive testing of our implementation of general relativistic force-free electrodynamics in Cartesian and spherical coordinates using the infrastructure of the E INSTEIN T OOLKIT . The employed hyperbolic/parabolic cleaning of numerical errors with full general relativistic compatibility allows for fast advection of numerical errors in dynamical spacetimes. Such fast advection of divergence errors significantly improves the stability of the general relativistic force-free electrodynamics modeling of BH magnetospheres.

79 ASTRONOMY AND ASTROPHYSICS↗