Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Electronic Structure Software”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4

Combining Physics and Machine Learning for the Next Generation of Molecular Simulation

Simulating molecules and atomic systems at quantum accuracy is a grand challenge for science in the 21 st century. Quantum-accurate simulations would enable the design of new medicines and the discovery of new materials. The defining problem in this challenge is that quantum calculations on large molecules, like proteins or DNA, are fundamentally impossible with current algorithms. In this work, we explore a range of different methods that aim to make large, quantum-accurate simulations possible. We show that using advanced classical models, we can accurately simulate ion channels, an important biomolecular system. We show how advanced classical models can be implemented in an exascale-ready software package. Lastly, we show how machine learning can learn the laws of quantum mechanics from data and enable quantum electronic structure calculations on thousands of atoms, a feat that is impossible for current algorithms. Altogether, this work shows that combining advances in physics models, computing, and machine learning, we are moving closer to the reality of accurately simulating our molecular world.

74 ATOMIC AND MOLECULAR PHYSICS↗

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

New Dimensions in the Theory of Excited States and X-ray Spectra (Final Report)

This Final Technical Report briefly summarizes the achievements during the lifetime of our DOE BES grant DE-FG02-97ER45623. The long-term goal of this project has been the development of quantitative theories of the interaction between radiation and matter, with a focus on x-ray spectroscopies. X-ray spectra have long been among the most important probes of atomic-scale structure and properties of matter, ranging from atoms and molecular systems to condensed matter and exotic states. These spectroscopies are widely used in investigations at the major DOE synchrotron x-ray facilities and related centers world-wide. In addition to fundamental theory, a major goal of our project has been the development of computational software that implements the theory for calculations of x-ray spectra of various materials throughout the periodic table. Due to the complex nature of x-ray spectra, quantitative theory is essential for its interpretation. The theory is challenging since it involves excited state electronic structure and many-body correlation effects that go beyond independent particle approximations like DFT or Hartree-Fock. Moreover, the experimental investigations typically involve a broad range of energy, time, and temperature scales, from the UV-Vis to hard x-ray energies of order 10 4 eV, and temperatures T from ambient up to the warm-dense-matter regime where the Fermi energy kBTF is of order a few eV, i.e., temperatures of order 105 Kelvin. This broad range of experimental conditions has fostered many novel theoretical approaches and computational techniques, many of which we have developed systematically over the duration of the grant. In contrast to the traditional wave-function approach of quantum theory and electronic structure methods, our theoretical approach is based on modern Green's function techniques. This approach is better suited for aperiodic structures, excited states, and broad spectral ranges, since it avoids the computational bottlenecks of sum-over-states approaches, as in the Fermi golden rule. This theoretical framework has been incorporated into efficient, user-friendly x-ray spectroscopy software which is now used routinely worldwide to simulate and analyze spectra. These theoretical tools provide an essential complement to synchrotron and next-generation light sources, which are used to investigate complex materials with ever increasing precision. Moreover, the synergism between theory, computation and experiment contributed by our research enhances scientific understanding and creates opportunities for innovations in materials and energy science and in many fields. As documented in this Report, this research grant has been remarkably successful in achieving these goals. In particular, this grant has supported the development of the x-ray spectroscopy software suite known as FEFF (named for an effective scattering amplitude f eff in the theory). The FEFF codes have become one of the premier tools for quantitative simulations of x-ray spectra as documented by many thousands of citations in the Web of Science and Google-Scholar.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Deep Space Systems Technology Program Future Deliveries

NASA is in a period of frequent launches of low cost deep space missions with challenging performance needs. The modest budgets of these missions make it impossible for each to develop its own technology, therefore, efficient and effective development and insertion of technology for these missions must be approached at a higher level than has been done in the past. The Deep Space Systems Technology Program (DSST), often referred to as X2000, has been formed to address this need. The program is divided into a series of "Deliveries" that develop and demonstrate a set of spacecraft system capabilities with broad applicability for use by multiple missions. The First Delivery Project, to be completed in 2001, will provide a one MRAD-tolerant flight computer, power switching electronics, efficient radioisotope power source, and a transponder with services at 8.4 GHz and 32 GHz bands. Plans call for a Second Delivery in late 2003 to enable complete deep space systems in the 10 to 50 kg class, and a Third Delivery built around Systems on a Chip (extreme levels of electronic and microsystems integration) around 2006. Formulation of Future Deliveries (past the First Delivery) is ongoing and includes plans for such developments as highly miniaturized digital/analog/power electronics, optical communications, multifunctional structures, miniature lightweight propulsion, advanced thermal control techniques, highly efficient radioisotope power sources, and a unified flight ground software architecture to support the needs of future highly intelligent space systems. All developments are targeted at broad applicability and reuse, and will be commercialized within the US.

Salvo, Christopher G.↗

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SMATool: Strength of materials analysis toolkit

The study of the strength of materials is a cornerstone in material science and engineering, playing a critical role in shaping the progress and application of materials in diverse industrial sectors. The strength of a material is meticulously examined to understand the behavior of the material under different stress conditions and environments, thereby guiding material selection and structural design. Herein, we introduce the SMATool, a computational toolkit for the efficient calculation and analysis of material strength at both zero and finite temperatures for 3D, 2D, 1D, and tubular 2D-based nanostructures and nanotubes, as well as 1D nanoribbons. The toolkit is capable of calculating tensile, shear, ultimate, yield, and indentation (Vickers' hardness) strengths in various dimensions, as well as the energy storage capacity. We conducted several calculations both at zero and finite temperatures to validate the accuracy and reliability of the developed software. Here, the results show that the SMATool package provides accurate predictions that align with existing data on material strength. SMATool integrates seamlessly with widely used electronic structure codes like VASP and Quantum Espresso, providing a user-friendly interface catering to academic researchers and industry professionals.

36 MATERIALS SCIENCE↗

Recent Developments in DFTB+, a Software Package for Efficient Atomistic Quantum Mechanical Simulations

DFTB+ is a flexible, open-source software package developed by its community, designed for fast and efficient atomistic quantum mechanical simulations. It employs various methods that approximate density functional theory (DFT), such as density functional-based tight binding (DFTB) and the extended tight binding (xTB) approach allowing simulations of large systems over extended time scales with reasonable accuracy, while being significantly faster than traditional ab initio methods. In recent years, several new extensions of the DFTB method have been developed and implemented in the DFTB+ program package in order to improve the accuracy and generality of the available simulation results. In this paper, we review those enhancements, show several use case examples and discuss the strengths and limitations of its features.

36 MATERIALS SCIENCE↗

Spectator Proton Detection and Reconstruction in Deep Inelastic D(E,EPS) Scattering

A Radial Time Projection Chamber (RTPC) was designed and installed in Jefferson Lab's Hall B as part of the BONuS12 (Barely Off-shell Nucleon Structure) experiment. The goal of BONuS12 is to accurately measure the structure function of the neutron by scattering 11 GeV electrons and detecting them with the CLAS12 spectrometer. Deuterium gas was used as an effective neutron target, and the new RTPC was used to detect low momentum spectator protons. Protons follow a curved path in the 5 Tesla solenoid that is part of CLAS12, ionizing the He-CO2 gas in an annular drift region surrounding the target. These ionization electrons are radially drifted outwards, amplified using cylindrical GEM (Gaseous Electron Multiplication) foils and recorded using readout pads located along the entire outer face of the cylindrical detector. The particle track reconstruction software discussed in detail in this thesis uses the signals from these pads to build tracks, which are reconstructed into the drift region using the arrival times of the signals and the positions of the pads. The proton momentum is measured from the track?s curvature and thus used to extract information about the struck neutron. This thesis introduces the theory of spectator tagging as an effective strategy for measuring neutron structure, by minimizing nuclear effects in the absence of a free neutron target. Along with discussing the many detectors that make up the CLAS12 spectrometer, the RTPC will be covered in detail, along with the tracking software designed to interpret the electronic signals to rebuild the low-momentum particle tracks, and fit them to extract the relevant kinematics. The results of the software, and preliminary analysis will be shown in the final chapter, as well as the discussion of possible improvements which could be made to the tracking software.

Payette, David↗

Quantum-Accurate Multiscale Modeling of Shock Hugoniots, Ramp Compression Paths, Structural and Magnetic Phase Transitions, and Transport Properties in Highly Compressed Metals

Fully characterizing high energy density (HED) phenomena using pulsed power facilities (Z machine) and coherent light sources is possible only with complementary numerical modeling for design, diagnostic development, and data interpretation. The exercise of creating numerical tests, that match experimental conditions, builds critical insight that is crucial for the development of a strong fundamental understanding of the physics behind HED phenomena and for the design of next generation pulsed power facilities. The persistence of electron correlation in HED materials arising from Coulomb interactions and the Pauli exclusion principle is one of the greatest challenges for accurate numerical modeling and has hitherto impeded our ability to model HED phenomena across multiple length and time scales at sufficient accuracy. An exemplar is a ferromagnetic material like iron, while familiar and widely used, we lack a simulation capability to characterize the interplay of structure and magnetic effects that govern material strength, kinetics of phase transitions and other transport properties. Herein we construct and demonstrate the Molecular-Spin Dynamics (MSD) simulation capability for iron from ambient to earth core conditions, all software advances are open source and presently available for broad usage. These methods are multi-scale in nature, direct comparisons between high fidelity density functional theory (DFT) and linear-scaling MSD simulations is done throughout this work, with advancements made to MSD allowing for electronic structure changes being reflected in classical dynamics. Main takeaways for the project include insight into the role of magnetic spins on mechanical properties and thermal conductivity, development of accurate interatomic potentials paired with spin Hamiltonians, and characterization of the high pressure melt boundary that is of critical importance to planetary modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Damage Detection Sensor System for Aerospace and Multiple Applications

NASA has identified structural health monitoring and damage detection and verification as critical needs in multiple technology roadmaps. The sensor systems can be customized for detecting location, damage size, and depth, with velocity options and can be designed for particular environments for monitoring of impact or physical damage to a structure. The damage detection system has been successfully demonstrated in a harsh environment and remote integration tested over 1000 miles apart. Multiple applications includes: Spacecraft and Aircraft; Inflatable, Deployable and Expandable Structures; Space Debris Monitoring; Space Habitats; Military Shelters; Solar Arrays, Smart Garments and Wearables, Extravehicular activity (EVA) suits; Critical Hardware Enclosures; Embedded Composite Structures; and Flexible Hybrid Printed Electronics and Systems. For better implementation and infusion into more flexible architectures, important and improved designs in advancing embedded software and GUI interface, and increasing flexibility, modularity, and configurable capabilities of the system are currently being carried out.

Williams, Martha↗

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗

Status of the JWST Science Instrument Payload

The James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM) system consists of five sensors (4 science): Mid-Infrared Instrument (MIRI), Near Infrared Imager and Slitless Spectrograph (NIRISS), Fine Guidance Sensor (FGS), Near InfraRed Camera (NIRCam), Near InfraRed Spectrograph (NIRSpec); and nine instrument support systems: Optical metering structure system, Electrical Harness System; Harness Radiator System, ISIM Electronics Compartment, ISIM Remote Services Unit, Cryogenic Thermal Control System, Command and Data Handling System, Flight Software System, Operations Scripts System.

JWST Payload↗

Forward Technology Solar Cell Experiment (FTSCE) for MISSE-5 Verified and Readied for Flight on STS-114

The Forward Technology Solar Cell Experiment (FTSCE) is a space solar cell experiment built as part of the Fifth Materials on the International Space Station Experiment (MISSE-5): Data Acquisition and Control Hardware and Software. It represents a collaborative effort between the NASA Glenn Research Center, the Naval Research Laboratory, and the U.S. Naval Academy. The purpose of this experiment is to place current and future solar cell technologies on orbit where they will be characterized and validated. This is in response to recent on-orbit and ground test results that raised concerns about the in-space survivability of new solar cell technologies and about current ground test methodology. The various components of the FTSCE are assembled into a passive experiment container--a 2- by 2- by 4-in. folding metal container that will be attached by an astronaut to the outer structure of the International Space Station. Data collected by the FTSCE will be relayed to the ground through a transmitter assembled by the U.S. Naval Academy. Data-acquisition electronics and software were designed to be tolerant of the thermal and radiation effects expected on orbit. The experiment has been verified and readied for flight on STS-114.

Jenkins, Phillip P.↗

2D Polyhedral Template Matching for Atomic Resolution Microscopy

SAND2024-13879O The 2D Polyhedral Template Matching for Atomic Resolution Microscopy is a suite of functions for analyzing atomic resolution electron microscopy images using the 2D polyhedral template matching (2D-PTM) method. This software analyzes atomic resolution microscopy data from electron microscopic imaging or scanning probe microscopies. The primary application is for identifying different crystal phases, crystal orientations, and defect structures obtained in such atomic resolution images. Written in MATLAB and starting from an atomic resolution image, the code identifies the positions of atomic intensity peaks. It then matches predefined structural templates to the local atomic environments. Outputs include the local structural identification, the template scaling factor and rotation angle, root-mean-squared deviation (RMSD), and centrosymmetry parameter.

Medlin, Douglas↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Implementation of Relativistic Coupled Cluster Theory for Massively Parallel GPU-Accelerated Computing Architectures

In this paper, we report reimplementation of the core algorithms of relativistic coupled cluster theory aimed at modern heterogeneous high-performance computational infrastructures. The code is designed for parallel execution on many compute nodes with optional GPU coprocessing, accomplished via the new ExaTENSOR back end. The resulting ExaCorr module is primarily intended for calculations of molecules with one or more heavy elements, as relativistic effects on the electronic structure are included from the outset. In the current work, we thereby focus on exact two-component methods and demonstrate the accuracy and performance of the software. The module can be used as a stand-alone program requiring a set of molecular orbital coefficients as the starting point, but it is also interfaced to the DIRAC program that can be used to generate these. We therefore also briefly discuss an improvement of the parallel computing aspects of the relativistic self-consistent field algorithm of the DIRAC program.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cartesian message passing neural networks for directional properties: Fast and transferable atomic multipoles

The message passing neural network (MPNN) framework is a promising tool for modeling atomic properties but is, until recently, incompatible with directional properties, such as Cartesian tensors. We propose a modified Cartesian MPNN (CMPNN) suitable for predicting atom-centered multipoles, an essential component of ab initio force fields. The efficacy of this model is demonstrated on a newly developed dataset consisting of 46 623 chemical structures and corresponding high-quality atomic multipoles, which was deposited into the publicly available Molecular Sciences Software Institute QCArchive server. We show that the CMPNN accurately predicts atom-centered charges, dipoles, and quadrupoles and that errors in the predicted atomic multipoles have a negligible effect on multipole–multipole electrostatic energies. The CMPNN is accurate enough to model conformational dependencies of a molecule’s electronic structure. This opens up the possibility of recomputing atomic multipoles on the fly throughout a simulation in which they might exhibit strong conformational dependence.

Glick, Zachary L. (ORCID:0000000309002849)↗

CASM Monte Carlo: Calculations of the thermodynamic and kinetic properties of complex multicomponent crystals

Monte Carlo techniques play a central role in statistical mechanics approaches that connect macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo techniques for the study of multicomponent crystalline materials within the Clusters Approach to Statistical Mechanics (CASM) software suite, and demonstrates their use in model systems to calculate free energies and kinetic coefficients, study phase transitions, and construct phase diagrams from first principles. Many crystal structures are complex, with multiple sublattices occupied by differing sets of chemical species, along with the presence of vacancies or interstitial species. This imposes constraints on concentration variables, the form of thermodynamic potentials, and the values of kinetic transport coefficients. The framework used by CASM to formulate thermodynamic potentials and kinetic transport coefficients accounting for arbitrarily complex crystal structures is presented and demonstrated with examples of increasing complexity. Additionally, an overview of the capabilities of the CASM software specific to Monte Carlo methods is given, and a new CASM software package is introduced, casm-flow, which helps automate the setup, submission, management, and analysis of Monte Carlo simulations.

Cluster expansion↗