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PySpawn: Software for Nonadiabatic Quantum Molecular Dynamics

The ab initio multiple spawning (AIMS) method enables nonadiabatic quantum molecular dynamics simulations in an arbitrary number of dimensions, with potential energy surfaces provided by electronic structure calculations performed on-the-fly. However, the intricacy of the AIMS algorithm complicates software development, deployment on modern shared computer resources, and post-simulation data analysis. PySpawn is a nonadiabatic molecular dynamics software package that addresses these issues. Here, the program is designed to be easily interfaced with electronic structure software, and an interface to the TeraChem software package is described here. PySpawn introduces a task-based reorganization of the AIMS algorithm, allowing fine-grained restart capability and setting the stage for efficient parallelization in a future release. PySpawn includes a user-friendly and interactive Python analysis module that will enable novice users to painlessly adopt AIMS. As a demonstration of PySpawn’s simulation capability and analysis module, we report complete active space self-consistent field–based AIMS simulations of the 1,2- dithienyl-1,2-dicyanoethene molecule, a promising molecular photoswitch.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Virtual Engineering Software Framework for Integrated Biomass Conversion Modeling

This presentation covers the design and implementation of a software tool to systematically connect computational models of unit operations to simulate an integrated process of low-temperature conversion of biomass to fuel. This virtual engineering (VE) software was designed with the overarching goal of connecting unit models written in various programming languages and requiring different computational resources within a single, flexible framework. The models and features currently considered for the VE library include mechanistic models for pretreatment, enzymatic hydrolysis, and aerobic bioreaction; high-fidelity computational fluid dynamics (CFD) simulations for enzymatic hydrolysis and aerobic bioreaction; and the capability to perform techno-economic analyses (TEA) using Aspen Plus, a commercial software package. The CFD models require access to high-performance computing (HPC) resources, so in addition to handling multiple programming languages and interfaces, the VE software must also be capable of interacting with an HPC scheduler to submit, run, and post-process jobs. Using the Python programming language, a new VE software package has been developed that contains functionality to manage the input-output communication between various unit models, schedule simulations to run on NREL's HPC and analyze those results, and interface with existing TEA software workflows. A Jupyter-notebook GUI was also created to solicit user input and provide documentation. In cases where multiple models for a particular unit-operation exist, selection between models is accomplished through a simple checkbox, with the appropriate inputs and outputs being parsed and converted seamlessly in the background. Each operation makes use of a different programming language, but the flow of information from pretreatment to enzymatic hydrolysis to bioreaction is managed with an intuitive, centralized file-communication strategy. In this talk, the programming approach and implementation details of the notebook are presented for multiple possibilities of the conversion process, including a demonstration of the ability to manage HPC resources. Additionally, an example of a sensitivity study of treatment parameters governing the overall conversion outcome is shown which highlights the ease of defining new problems using the VE Notebook workflow and leads into a discussion of ongoing work to enable outer-loop optimization studies.

biofuel↗

Systematic Benchmarking of Climate Models: Methodologies, Applications, and New Directions

As climate models become increasingly complex, there is a growing need to comprehensively and systematically assess model performance with respect to observations. Given the increasing number and diversity of climate model simulations in use, the community has moved beyond simple model intercomparison and toward developing methods capable of benchmarking a large number of simulations against a suite of climate metrics. Here, we present a detailed review of evaluation and benchmarking methods and approaches developed in the last decade, focusing primarily on scientific implications for Coupled Model Intercomparison Project (CMIP) simulations and CMIP6 results that contributed to the Intergovernmental Panel on Climate Change (IPCC) Sixth Assessment Report (AR6). Based on this review, we explain the resulting contemporary philosophy of model benchmarking, and provide clear distinctions and definitions of the terms model verification, process validation, evaluation, and benchmarking. While significant progress has been made in model development based on systematic evaluation and benchmarking efforts, some climate system biases still remain. The development of open‐source community software packages has played a fundamental role in identifying areas of significant model improvement and bias reduction. We review the key features of several software packages that have been commonly used over the past decade to evaluate and benchmark global and regional climate models. Additionally, we discuss best practices for the selection of evaluation and benchmarking metrics and for interpreting the obtained results, the importance of selecting suitable sources of reference data and accurate uncertainty quantification.

Environmental sciences↗

XtalCAMP: a comprehensive program for the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data

XtalCAMP is a software package based on the MATLAB platform, which is suitable for, but not limited to, the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data. The main objective of the software is to provide complementary functionalities to the Laue indexing software packages used at several synchrotron beamlines. Here, the graphical user interfaces allow the easy analysis of characteristic microstructure features, including real-time intensity mapping for a quick examination of phase, grain and defect distribution, 2D color-coded mapping of microstructural properties from the output of other Laue indexing software, crystal orientation visualization, grain boundary characterization based on orientation/misorientation calculation, principal strain/stress analysis, and strain ellipsoid representation, as well as a series of additional toolkits. As an example, XtalCAMP is applied to the microstructural investigation of a solution-heat-treated Ni-based superalloy manufactured using a laser 3D-printing technique, and a deformed natural quartzite from Val Bregaglia in the Central Alps.

36 MATERIALS SCIENCE↗

300_underground robot (final research report)

Recent advancements in mobile robotics have displayed impressive capabilities in traversing and accessing areas that are inaccessible to humans either due to the characteristics of the environment or potential hazards. Furthermore, these advancements within the field of mobile robotics, more specifically uncrewed ground vehicles (UGVs), give the ability to potentially survey, observe, and map these inaccessible areas for humans. However, one of the most challenging areas to implement this technology is underground environments. The main challenge with implementing this technology in underground environments is the dependence on either GPS or RF communication for UGVs to navigate properly. Therefore, in order to properly demonstrate the mapping capabilities of the UGV this challenge must be resolved. The overall goal of this study is to demonstrate the mapping capabilities of a UGV while addressing this challenge and documenting the implementation and testing phase of the robot. The proposed solution to this challenge is to implement a SLAM algorithm onto the main computational device of the UGV utilizing the Robot Operating System (ROS). The algorithm is the open-source software package Slam Toolbox developed by Steve Macenski. Furthermore, the sllidar_ros2 package from Slamtec will be used to gather the lidar data from an A3M1 2D lidar. A separate program will be created to gather odometry information for our UGV robot. All of these software packages will run together in a Docker environment. Through working on this project I have developed a better understanding of the world of robotics/autonomous systems, especially with applications such as navigation and mapping. Furthermore, through this project, I have been given exposure to how research is conducted within a DOE lab setting. As robotics/autonomous systems become more advanced it's important to pursue more avenues of research such as this project as it will ensure the development of our capabilities.

42 ENGINEERING↗

Sensitivity-based Similarity Metrics for New Experiment Design Optimization

The nuclear data used in advanced reactor simulations requires validation. Data from nuclear criticality experiments can provide this validation. New nuclear criticality experiment design requires extensive knowledge and expert judgement such that the experimental design parameters are selected in such a way to keep the experiment subcritical. To aide in this experimental design process, professionals can utilize sensitivity and uncertainty analysis. Sensitivity and uncertainty analysis relies on matching new application experiments with currently existing benchmark experiments. Currently, there is functionality in the Whisper 1.1 software package to calculate a similarity metric based on neutron multiplication factor sensitivity coefficients between a new application designed by the user and existing International Criticality Safety Benchmark Experiment Project (ICSBEP) benchmarks. The Whisper 1.1 software package is included in Monte Carlo N-Particle ® Code Version 6.21 (MCNP ® 6.2). This work is geared toward expanding this capability to new similarity metrics based on beta-effective sensitivity coefficients and reactivity coefficient sensitivity coefficients. While the investigation of these sensitivity coefficients is presented in detail in separate works at this same conference, this work will be primarily focused on studying the similarity metrics in more detail. These similarity metrics will then be incorporated into the optimization algorithms used for experiment design in EUCLID (Experiments Underpinned by Computational Learning for Improvements in nuclear Data), which is a Los Alamos National Laboratory (LANL) project designed to constrain nuclear data of interest, such that adjustments can be made to possible inaccuracies. A more detailed optimization can be subsequently performed by breaking down these similarity metrics by isotope, reaction, and energy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

VAN-DAMME: GPU-accelerated and symmetry-assisted quantum optimal control of multi-qubit systems

We present an open-source software package, VAN-DAMME (Versatile Approaches to Numerically Design, Accelerate, and Manipulate Magnetic Excitations), for massively-parallelized quantum optimal control (QOC) calculations of multi-qubit systems. To enable large QOC calculations, the VAN-DAMME software package utilizes symmetry-based techniques with custom GPU-enhanced algorithms. This combined approach allows for the simultaneous computation of hundreds of matrix exponential propagators that efficiently leverage the intra-GPU parallelism found in high-performance GPUs. In addition, to maximize the computational efficiency of the VAN-DAMME code, we carried out several extensive tests on data layout, computational complexity, memory requirements, and performance. These extensive analyses allowed us to develop computationally efficient approaches for evaluating complex-valued matrix exponential propagators based on Padé approximants. To assess the computational performance of our GPU-accelerated VAN-DAMME code, we carried out QOC calculations of systems containing 10 - 15 qubits, which showed that our GPU implementation is 18.4× faster than the corresponding CPU implementation. Our GPU-accelerated enhancements allow efficient calculations of multi-qubit systems, which can be used for the efficient implementation of QOC applications across multiple domains.

97 MATHEMATICS AND COMPUTING↗

Implementing Ordinary Differential Equation Solvers in Rust Programming Language for Modeling Vehicle Powertrain Systems: Preprint

Efficient and accurate ordinary differential equation (ODE) solvers are necessary for powertrain and vehicle dynamics modeling. However, current commercial ODE solvers can be financially prohibitive, leading to a need for accessible, effective, open-source ODE solvers designed for powertrain modeling. Rust is a compiled programming language that has the potential to be used for fast and easy-to-use powertrain models, given its exceptional computational performance, robust package ecosystem, and short time required for modelers to become proficient. However, of the three commonly used (>3,000 downloads) packages in Rust with ODE solver capabilities, only one has more than four numerical methods implemented, and none are designed specifically for modeling physical systems. Therefore, the goal of the Differential Equation System Solver (DESS) was to implement accurate ODE solvers in Rust designed for the component-based problems often seen in powertrain modeling. DESS is a text-based software package that provides a flexible framework for building and solving systems of ODEs. This allows DESS to be included as a dependency for automotive powertrain models that require a variety of solvers and solver configurations. Seven explicit ODE solver methods have been implemented in DESS: Euler’s, Heun’s, midpoint, Ralston’s, classic Runge-Kutta, Bogacki-Shampine, and Cash-Karp. These represent five fixed-step methods and two adaptive-step methods. This paper shows that the solver implementations increase accuracy and computational efficiency compared to Euler's method when modeling a system of three thermal masses in Rust. DESS also includes features designed for modeling component-based physical systems. Users can define relationships between nodes in their system, which the package then translates into a system of equations, leading to simpler and more intuitive code. In the case of a three-thermal-mass system, the user can specify node thermal properties (e.g., thermal capacitance), how nodes are interconnected, and thermal conductance between nodes rather than providing a system of equations. The core contribution from this work is an open-source, text-based Rust package with ODE solvers for automotive powertrain modeling to support cost-free, fast, and accurate simulation.

ADVANCED PROPULSION SYSTEMS↗

NESSi : The N on- E quilibrium S ystems S imulation package

The nonequilibrium dynamics of correlated many-particle systems is of interest in connection with pump–probe experiments on molecular systems and solids, as well as theoretical investigations of transport properties and relaxation processes. Nonequilibrium Green’s functions are a powerful tool to study interaction effects in quantum many-particle systems out of equilibrium, and to extract physically relevant information for the interpretation of experiments. Here, we present the open-source software package NESSi (The Non-Equilibrium Systems Simulation package) which allows to perform many-body dynamics simulations based on Green’s functions on the L-shaped Kadanoff–Baym contour. NESSi contains the library libcntr which implements tools for basic operations on these nonequilibrium Green’s functions, for constructing Feynman diagrams, and for the solution of integral and integro-differential equations involving contour Green’s functions. The library employs a discretization of the Kadanoff–Baym contour into time points and a high-order implementation of integration routines. The total integrated error scales up to $\mathcal{O}(N^{-7})$, which is important since the numerical effort increases at least cubically with the simulation time. A distributed-memory parallelization over reciprocal space allows large-scale simulations of lattice systems. We provide a collection of example programs ranging from dynamics in simple two-level systems to problems relevant in contemporary condensed matter physics, including Hubbard clusters and Hubbard or Holstein lattice models. The libcntr library is the basis of a follow-up software package for nonequilibrium dynamical mean-field theory calculations based on strong-coupling perturbative impurity solvers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The use of subchondral bone topography to approximate the center of rotation of the elbow joint in dogs

Abstract Objectives The aim of this study was to compare the approximate center of rotation in normal and diseased elbows in dogs. Study design Cross‐sectional study Sample population Computer tomography scans of nine dogs with unilateral fragmented medial coronoid process (FMCP). Methods A board certified radiologist confirmed that each dog had unilateral FMCP, and a normal contralateral elbow. Digital 3D models of all elbow joints were uploaded into a surgical planning software package. Four axes approximating the center of rotation (COR) of elbow joints were generated using five geometric shapes based on subchondral topography of the humeral condyle radius and ulna. Images showing the locations where axes exited the medial and lateral cortex of the humeral condyle were captured and imported into a second software package, for measurement of distances between exit points and the origin of a system of axes. Results In normal joints 20/27 (74%) axes exited the medial cortex, and 25/27 (93%) axes exited the lateral cortex cranial and distal to the medial and lateral epicondyles, respectively. In diseased joints 22/27 (81%) axes exited medial cortex and 19/27 (70%) axes exited the lateral cortex, caudal and distal to the medial and lateral epicondyles, respectively. Conclusion Based on CT‐ derived geometry, the COR of elbow affected with FMCP was generally more caudal than normal. Clinical significance External landmarks approximating the location of the elbow COR are provided, and while not validated, may assist in planning, creation, and assessment of procedures for FMCP.

Berger, Chen↗

Focused Ion Beam Tomography of Alloy 617 Corroded in Molten Chloride Salt

Materials qualification of reactor structural materials is a critical step in rapid implementation of advanced nuclear reactor technologies, particularly to assess the corrosion performance in these designs. Accelerated qualification of reactor structural materials requires incorporating powerful computational toolsets, such as phase field modelling in the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework, to predict the evolution of structural materials due to corrosion. Accordingly, computational toolsets will require experimental data generated at appropriate length scales to validate accuracy. Focused ion beam (FIB) provides a high degree of control over manipulation of materials for analytical purposes, including capturing data on the evolution in the microstructure and elemental composition of materials at the mesoscale, an appropriate length scale for phase field modelling of intergranular diffusion phenomena using the MOOSE framework. For instance, the FEI Helios G4 UX dual beam plasma FIB microscope at the Irradiated Materials Characterization Laboratory (IMCL) is capable of backscatter diffraction (EBSD) and energy-dispersive x-ray spectroscopy (EDS) documenting the evolution in the microstructure and elemental composition, respectively. The Helios can perform EDS and EBSD three-dimensionally (3D) using tomography, which is then combined using different software packages to visualize 3D volumes correlating elemental composition to microstructural data. The purpose of this investigation was to develop a streamlined characterization and data processing workflow for 3D tomography studies on the FEI Helios G4 plasma FIB. The investigation is segmented into three parts: 1) Optimizing the data collection workflow, 2) identifying appropriate data processing and visualization software (i.e. DREAM.3D, MIPAR, and VGStudioMax), and 3) establishing an infrastructure for public release. The optimization of the data collection workflow is in collaboration with members of the U220 department to setup formal training on the tomography operation of the G4, through ThermoFisher Scientific, and exploring DREAM.3D, MIPAR, and VGStudioMax data processing/visualization software packages. VGStudioMax currently demonstrates the most promise for future use. Optimization of the data collection and processing workflow is still ongoing. A collaboration with INL High Performance Computing (HPC) established an open-source license for expediting the public release of FIB tomography datasets through HPC. FIB tomography data generated by the G4 will provide comprehensive data for validating 3D phase field mesoscale modelling tools within the MOOSE framework for accelerated qualification of reactor structural materials.

Copeland-Johnson, Trishelle↗

Grey-box modeling and application for building energy simulations - A critical review

Grey-box modeling, as one of the three fundamental modeling techniques for building energy models, has many advantages compared with black-box modeling and white-box modeling. Additionally, it has been widely applied to solve problems of building technologies, such as building load estimation, control and optimization, and building-grid integration. However, a thorough review of grey-box modeling is not available. This review study systematically investigated various aspects of grey-box modeling for buildings. First, the fundamental aspects of grey-box modeling are presented, including the theoretical background, modeling of building elements, modeling order, modeling diagram, and order reduction. Second, the detailed modeling approaches are discussed. Third, multiple applications of grey-box modeling are investigated for building energy domain, which are categorized into the following groups: heat dynamics analysis, thermal load estimation, building control and optimization, district/urban scale energy modeling, and building-grid integration. Finally, the available software packages for grey-box modeling are compared. Overall, the challenges of using grey-box modeling can be summarized as follows: (1) the theoretical limitations and assumptions of grey-box modeling are unclear; (2) grey-box model naming convention and structure are confusing; (3) grey-box model creation is vague; (4) suitable applications of grey-box models are unknown; and (5) grey-box models lack unified software solutions for wider adoption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Generalizable, fast, and accurate DeepQSPR with fastprop

Abstract Quantitative Structure–Property Relationship studies (QSPR), often referred to interchangeably as QSAR, seek to establish a mapping between molecular structure and an arbitrary target property. Historically this was done on a target-by-target basis with new descriptors being devised to specifically map to a given target. Today software packages exist that calculate thousands of these descriptors, enabling general modeling typically with classical and machine learning methods. Also present today are learned representation methods in which deep learning models generate a target-specific representation during training. The former requires less training data and offers improved speed and interpretability while the latter offers excellent generality, while the intersection of the two remains under-explored. This paper introduces , a software package and general Deep-QSPR framework that combines a cogent set of molecular descriptors with deep learning to achieve state-of-the-art performance on datasets ranging from tens to tens of thousands of molecules. provides both a user-friendly Command Line Interface and highly interoperable set of Python modules for the training and deployment of feedforward neural networks for property prediction. This approach yields improvements in speed and interpretability over existing methods while statistically equaling or exceeding their performance across most of the tested benchmarks. is designed with Research Software Engineering best practices and is free and open source, hosted at github.com/jacksonburns/fastprop.

Burns, Jackson W. (ORCID:0000000206579426)↗

Reinforcement Learning for Distribution Grid Optimization (PyCIGAR) v0.1

PyCIGAR is a python software package that merges off-the-shelf reinforcement learning libraries (RLLib and Ray) with electric power distribution system simulation tools (OpenDSS and a custom power flow solver built by LBL). PyCIGAR enables the training of neural networks to optimize the behavior of different components in the electric distribution grid, such as control systems in photovoltaic rooftop solar inverters and electric battery storage systems. The software package has been used to train neural networks to update settings in photovoltaic rooftop solar inverter control systems to mitigate cyber attacks on other solar photovoltaic rooftop devices.

Arnold, Daniel↗

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↗

Guideline 36 Savings Calculator v0.1

This software package contains a simple calculator that can be used to estimate savings from implementing a retrofit of HVAC controls to ASHRAE Guideline 36 in a multi-zone office building. Implemented in Excel, the calculator has a user-interface front-end to configure parameters of the case study, such as location, building size, and existing control strategies, and a back-end containing results from a large number of pre-run annual energy simulations. The software package also contains the simulation models and associated pre- and post-processing scripts to generate these results.

Blum, David↗

Nuclear Criticality Safety Integral Experiment Covariance Determination

Integral benchmarks for criticality safety and nuclear data validation require expensive uncertainty quantification studies. Commonly, the uncertainty quantification ignores correlations between experiments that share components. Experiments such as the TEX (Thermal/Epithermal eXperiments) campaigns consist of many shared parts between experiments, such as fuel, which creates a strong correlation in their errors. While these correlations are known to exist, they are often not estimated due to the complexity of such calculations. This paper describes a software package that uses an intuitive method of determining the covariance for each of the experimental components, providing a correlation matrix for each family of parts across the multiple cases examined within a benchmark. The code uses the TEX-HEU campaign as a proof of concept, and we show that the correlations can be calculated with information commonly found in ICSBEP (International Criticality Safety Benchmark Evaluation Project) benchmarks. The estimated covariances are used in χ 2 trending studies to evaluate their impact on nuclear data validation. The covariance determination code can be easily integrated into current benchmark evaluations as well as reevaluating legacy benchmark uncertainties. Uncertainty correlation calculations should become the baseline for criticality safety integral experiment benchmarks and can now be easily calculated with the described software package.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Rapid generation of optimal generalized Monkhorst-Pack grids

In this report computational modeling of the properties of crystalline materials has become an increasingly important aspect of materials research, consuming hundreds of millions of CPU-hours at scientific computing centers around the world each year, if not more. A routine operation in such calculations is the evaluation of integrals over the Brillouin zone. We have previously demonstrated that performing such integrals using generalized Monkhorst-Pack k-point grids can roughly double the speed of these calculations relative to the widely-used traditional Monkhorst-Pack grids. However the generation of optimal generalized Monkhorst-Pack grids is not implemented in most software packages due to the computational cost and difficulty of identifying the best grids. To address this problem, we present new algorithms that allow rapid generation of optimal generalized Monkhorst-Pack grids on the fly. We demonstrate that the grids generated by these algorithms are on average significantly more efficient than those generated using existing algorithms across a range of grid densities. For grids that correspond to a real-space supercell with at least 50 Å between lattice points, which is sufficient to converge density functional theory calculations within 1 meV/atom for nearly all materials, our algorithm finds optimized grids in an average of 0.19 s on a single processing core. To facilitate the widespread adoption of this approach, we present new open-source tools including a library designed for integration with third-party software packages.

36 MATERIALS SCIENCE↗