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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

A simple solution to the Rietveld refinement recipe problem

Rietveld refinements are widely used for many purposes in the physical sciences. Conducting a Rietveld refinement typically requires expert input because correct results may require that parameters be added to the fit in the proper order. This order will depend on the nature of the data and the initial parameter values. A mechanism for computing the next parameter to add to the refinement is shown. The fitting function is evaluated with the current parameter value set and each parameter incremented and decremented by a small offset. This provides the partial derivatives with respect to each parameter, along with information to discriminate meaningful values from numerical computational errors. The implementation of this mechanism in the open-source GSAS-II program is discussed. This new method is discussed as an important step towards the development of automated Rietveld refinement technology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Scalable Algorithms for Distributed-Memory Adaptive Mesh Refinement

This paper presents scalable algorithms and data structures for adaptive mesh refinement computations. We describe a novel mesh restructuring algorithm for adaptive mesh refinement computations that uses a constant number of collectives regardless of the refinement depth. To further increase scalability, we describe a localized hierarchical coordinate-based block indexing scheme in contrast to traditional linear numbering schemes, which incur unnecessary synchronization. In contrast to the existing approaches which take O(P) time and storage per process, our approach takes only constant time and has very small memory footprint. With these optimizations as well as an efficient mapping scheme, our algorithm is scalable and suitable for large, highly-refined meshes. We present strong-scaling experiments up to 2k ranks on Cray XK6, and 32k ranks on IBM Blue Gene/Q.

Langer, Akhil↗
DOE OSTI2012

Liver segmentation in contrast enhanced CT data using graph cuts and interactive 3D segmentation refinement methods

Purpose: Liver segmentation is an important prerequisite for the assessment of liver cancer treatment options like tumor resection, image-guided radiation therapy (IGRT), radiofrequency ablation, etc. The purpose of this work was to evaluate a new approach for liver segmentation. Methods: A graph cuts segmentation method was combined with a three-dimensional virtual reality based segmentation refinement approach. The developed interactive segmentation system allowed the user to manipulate volume chunks and/or surfaces instead of 2D contours in cross-sectional images (i.e, slice-by-slice). The method was evaluated on twenty routinely acquired portal-phase contrast enhanced multislice computed tomography (CT) data sets. An independent reference was generated by utilizing a currently clinically utilized slice-by-slice segmentation method. After 1 h of introduction to the developed segmentation system, three experts were asked to segment all twenty data sets with the proposed method. Results: Compared to the independent standard, the relative volumetric segmentation overlap error averaged over all three experts and all twenty data sets was 3.74%. Liver segmentation required on average 16 min of user interaction per case. The calculated relative volumetric overlap errors were not found to be significantly different [analysis of variance (ANOVA) test, p = 0.82] between experts who utilized the proposed 3D system. In contrast, the time required by each expert for segmentation was found to be significantly different (ANOVA test, p = 0.0009). Major differences between generated segmentations and independent references were observed in areas were vessels enter or leave the liver and no accepted criteria for defining liver boundaries exist. In comparison, slice-by-slice based generation of the independent standard utilizing a live wire tool took 70.1 min on average. A standard 2D segmentation refinement approach applied to all twenty data sets required on average 38.2 min of user interaction and resulted in statistically not significantly different segmentation error indices (ANOVA test, significance level of 0.05). Conclusions: All three experts were able to produce liver segmentations with low error rates. User interaction time savings of up to 71% compared to a 2D refinement approach demonstrate the utility and potential of our approach. The system offers a range of different tools to manipulate segmentation results, and some users might benefit from a longer learning phase to develop efficient segmentation refinement strategies. The presented approach represents a generally applicable segmentation approach that can be applied to many medical image segmentation problems.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

PRISMA: PARALLEL REFINEMENT AND INTEGRATION SYSTEM FOR MULTI-AZIMUTHAL ANALYSIS

The Parallel Refinement and Integration System for Multi-azimuthal Analysis (PRISMA, version 1.1.0) is a Python application for processing X-ray diffraction (XRD) image data. PRISMA wraps GSAS-II to perform azimuthally-binned peak refinement, computes per-frame strain and d-spacing from those fits, and provides three PyQt5 graphical interfaces: (1) a Recipe Builder for selecting GSAS-II control (.imctrl) files, optional mask (.immask) files or threshold-ased masking, reference and experiment image sets, peaks, zimuthal range and bin size, and an optional ceria-based auto-calibration; (2) a Batch Processor that uses Dask on local workstations and pure MPI (mpi4py.futures.MPICommExecutor) on HPC to distribute GSAS-II refinement across cores or compute nodes and write results to a 4-dimensional (peaks x frames x azimuths x measurements) Zarr dataset; and (3) a Data Analyzer that renders heatmaps of fit parameters, strain, frame-to-frame deltas, and percent-change-vs-reference, and exports user-defined subsections to CSV or Excel. The peak-refinement algorithm is deterministic. Benchmark on ALCF Crux: a 20,000-image set, single-peak fit in frame mode with 44 azimuthal bins on 128 nodes x 128 workers, 48 seconds total wall time.

Lorenzo Martin, Maria De La Cinta [Argonne Nationa↗
DOE OSTI2017

Assessment of Vertical Mesh Refinement in Concurrently Nested Large-Eddy Simulations Using the Weather Research and Forecasting Model

To facilitate multiscale simulation using the Weather Research and Forecasting Model, vertical mesh refinement for one-way concurrent nested simulation was recently introduced. Grid refinement in the vertical dimension removes the requirement of different grid aspect ratios on the bounding versus the nested domain, such that results from refinement are in the horizontal directions only, and thereby can also reduce numerical errors on the bounding domain arising from large aspect ratios in the presence of complex terrain. Herein, the impacts of vertical grid refinement on the evolving downstream flow in nested large-eddy simulations are evaluated in relation to other model configuration choices, including turbulence subfilter-scale (SFS) stress models, mesh configuration, and alternative methods for calculating several near-surface flow parameters. Although vertical nesting requires coarsening of the vertical grid on the bounding domain, leading to a smaller range of resolved turbulence scales in the nest’s lateral boundary conditions, parameter values within the nested domains are generally only minimally impacted, relative to nesting using the same vertical grid on each domain. Two dynamic SFS models examined herein generally improved the simulated mean wind speed, turbulence kinetic energy, stresses and spectra, on both domains, and accelerated equilibration rates within nested domains, relative to two constant coefficient models. A new method of extrapolating horizontal velocity components to near-surface locations at nested domain lateral boundaries, and a correction to the calculation of deformation elements near the surface, are each shown to slightly alter the mean parameter values, yet only minimally impact equilibration rates within the nested domain.

14 SOLAR ENERGY↗
DOE OSTI2022

Historical review and proof-of-concept future method demonstration of adaptive mesh refinement in nuclear engineering for increased fidelity and computational efficiency

As the nuclear industry's use of computational tool increases, the need for increased fidelity and computational efficiency is well known. While most approaches to increased fidelity rely on applying a fine mesh over the problem domain, a more efficient method is to apply an adaptive mesh refinement (AMR) algorithm to the mesh definition. In the field of nuclear engineering, AMR has previously been used in conjunction with deterministic methods, including: S{sub N} transport methods, Lattice Boltzmann Methods, and COMSOL. The future of AMR in nuclear engineering is to couple it to a Monte Carlo code with the goal of reducing calculation time. A proof-of-concept example yielded positive results for using the gradient of the flux as a refinement criteria. The refinement criteria was varied from 0.01 to 0.10, which yielded a recommended range of 0.01 to 0.04, and the number of refinement iterations was varied from 0 to 7, with diminishing returns seen after 5 iterations. After the success of the proof-of-concept exercise, work began on creating a full program coupling MCNP6.2 and the AMR algorithm in the deal.II library. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2015

Use Case Realization Report: UCR-03.02 Refines Event

This architecturally significant use case describes how the Analyst refines an event hypothesis. The Analyst checks waveform quality (see 'Determines Waveform Data Quality' UC). For waveforms of sufficient quality, the Analyst enhances signals and suppresses noise on waveforms for relevant stations (see 'Enhances Signals' UC), adds and associates missing detections, and modifies or unassociates detections already associated with the event hypothesis (see 'Detects Signals' UC). The Analyst rejects event hypotheses that are invalid. For valid event hypotheses, the Analyst measures signal features associated with the detections (see 'Measures Signal Features' UC) and evaluates the moment tensor ('Evaluates Moment Tensor' UC). The Analyst uses these signal features to refine the location (see 'Refines Event Location' UC) and magnitude (see 'Refines Event Magnitude' UC) of the event hypothesis. The Analyst compares events to determine how similar events were constructed (see 'Compares Events' UC). The Analyst repeats these steps until satisfied with the results. Analysts may provide feedback for previous Analysts during any of these steps (see 'Provides Analyst Feedback' UC). This use case is architecturally significant because it captures the interplay between all of the Analyst activities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Grain Refinement Effect on the Hot-Tearing Resistance of Higher-Temperature Al–Cu–Mn–Zr Alloys

The hot-tearing resistance of Al-Cu-Mn-Zr (ACMZ) alloys was investigated as a step toward introducing these new cast alloys for severe duty, higher-temperature applications, such as cylinder heads for down-sized, turbocharged automotive engines. Alloy Cu compositions were varied from 5 to 8 wt.%. Targeted Ti levels were 0.02, 0.1, and 0.2 wt.% via additions of the Al–5Ti–1B master alloy. Hot-tearing resistance was assessed by visual examination and ranking of the cracking severity in a multi-arm permanent mold casting. It was found that at high impurity contents (Fe and Si of 0.2 wt.% each), the Al–Cu–Mn–Zr alloy with 4.95 wt.% Cu exhibited the poorest hot-tearing resistance, irrespective of the grain refining amount. Microstructural analysis indicated an effective reduction in the grain size, as the Ti additions were increased to 0.02 and 0.1 wt.% Ti via the Al–Ti–B grain refiner. The finest grain size was attained with a 0.1 wt.% Ti. Based on the hot-tearing evaluation, it was found that the additional grain refining via the Al–5Ti–1B master alloy at 0.1 wt.% Ti significantly reduces the hot-tearing susceptibility at Cu contents greater than 7.3 wt.% for ACMZ alloys with low Fe and Si. These findings indicate that the best hot-tearing resistance was observed at a grain refiner level of 0.1 wt.% Ti and high Cu content (greater than 7.3 wt.%). This study to indicates that these Al–Cu–Mn–Zr alloys, which possess excellent microstructural stability and mechanical properties at elevated temperatures, can also possess excellent hot-tearing resistance.

36 MATERIALS SCIENCE↗
NASA NTRS1989

Vortex-dominated conical-flow computations using unstructured adaptively-refined meshes

A conical Euler/Navier-Stokes algorithm is presented for the computation of vortex-dominated flows. The flow solver involves a multistage Runge-Kutta time stepping scheme which uses a finite-volume spatial discretization on an unstructured grid made up of triangles. The algorithm also employs an adaptive mesh refinement procedure which enriches the mesh locally to more accurately resolve the vortical flow features. Results are presented for several highly-swept delta wing and circular cone cases at high angles of attack and at supersonic freestream flow conditions. Accurate solutions were obtained more efficiently when adaptive mesh refinement was used in contrast with refining the grid globally. The paper presents descriptions of the conical Euler/Navier-Stokes flow solver and adaptive mesh refinement procedures along with results which demonstrate the capability.

Batina, John T.↗
NASA NTRS1989

Mesh refinement in finite element analysis by minimization of the stiffness matrix trace

Most finite element packages provide means to generate meshes automatically. However, the user is usually confronted with the problem of not knowing whether the mesh generated is appropriate for the problem at hand. Since the accuracy of the finite element results is mesh dependent, mesh selection forms a very important step in the analysis. Indeed, in accurate analyses, meshes need to be refined or rezoned until the solution converges to a value so that the error is below a predetermined tolerance. A-posteriori methods use error indicators, developed by using the theory of interpolation and approximation theory, for mesh refinements. Some use other criterions, such as strain energy density variation and stress contours for example, to obtain near optimal meshes. Although these methods are adaptive, they are expensive. Alternatively, a priori methods, until now available, use geometrical parameters, for example, element aspect ratio. Therefore, they are not adaptive by nature. An adaptive a-priori method is developed. The criterion is that the minimization of the trace of the stiffness matrix with respect to the nodal coordinates, leads to a minimization of the potential energy, and as a consequence provide a good starting mesh. In a few examples the method is shown to provide the optimal mesh. The method is also shown to be relatively simple and amenable to development of computer algorithms. When the procedure is used in conjunction with a-posteriori methods of grid refinement, it is shown that fewer refinement iterations and fewer degrees of freedom are required for convergence as opposed to when the procedure is not used. The mesh obtained is shown to have uniform distribution of stiffness among the nodes and elements which, as a consequence, leads to uniform error distribution. Thus the mesh obtained meets the optimality criterion of uniform error distribution.

Kittur, Madan G.↗
NASA NTRS1990

Finite element mesh refinement criteria for stress analysis

This paper discusses procedures for finite-element mesh selection and refinement. The objective is to improve accuracy. The procedures are based on (1) the minimization of the stiffness matrix race (optimizing node location); (2) the use of h-version refinement (rezoning, element size reduction, and increasing the number of elements); and (3) the use of p-version refinement (increasing the order of polynomial approximation of the elements). A step-by-step procedure of mesh selection, improvement, and refinement is presented. The criteria for 'goodness' of a mesh are based on strain energy, displacement, and stress values at selected critical points of a structure. An analysis of an aircraft lug problem is presented as an example.

Kittur, Madan G.↗
NASA NTRS1991

Unstructured Euler flow solutions using hexahedral cell refinement

An attempt is made to extend grid refinement into three dimensions by using unstructured hexahedral grids. The flow solver is developed using the TIGER (topologically Independent Grid, Euler Refinement) as the starting point. The program uses an unstructured hexahedral mesh and a modified version of the Jameson four-stage, finite-volume Runge-Kutta algorithm for integration of the Euler equations. The unstructured mesh allows for local refinement appropriate for each freestream condition, thereby concentrating mesh cells in the regions of greatest interest. This increases the computational efficiency because the refinement is not required to extend throughout the entire flow field.

Melton, John E.↗
NASA NTRS1991

An adaptively-refined Cartesian mesh solver for the Euler equations

A method for adaptive refinement of a Cartesian mesh for the solution of the steady Euler equations is presented. The algorithm creates an initial uniform mesh and cuts the body out of that mesh. The mesh is then refined based on body curvature. Next, the solution is converged to a steady state using a linear reconstruction and Roe's approximate Riemann solver. Solution-adaptive refinement of the mesh is then applied to resolve high-gradient regions of the flow. The numerical results presented show the flexibility of this approach and the accuracy attainable by solution-based refinement.

De Zeeuw, Darren↗
NASA NTRS1994

An Adaptively-Refined, Cartesian, Cell-Based Scheme for the Euler and Navier-Stokes Equations

A Cartesian, cell-based scheme for solving the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, polygonal 'cut' cells are created. The geometry of the cut cells is computed using polygon-clipping algorithms. The grid is stored in a binary-tree data structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded, with a limited linear reconstruction of the primitive variables used to provide input states to an approximate Riemann solver for computing the fluxes between neighboring cells. A multi-stage time-stepping scheme is used to reach a steady-state solution. Validation of the Euler solver with benchmark numerical and exact solutions is presented. An assessment of the accuracy of the approach is made by uniform and adaptive grid refinements for a steady, transonic, exact solution to the Euler equations. The error of the approach is directly compared to a structured solver formulation. A non smooth flow is also assessed for grid convergence, comparing uniform and adaptively refined results. Several formulations of the viscous terms are assessed analytically, both for accuracy and positivity. The two best formulations are used to compute adaptively refined solutions of the Navier-Stokes equations. These solutions are compared to each other, to experimental results and/or theory for a series of low and moderate Reynolds numbers flow fields. The most suitable viscous discretization is demonstrated for geometrically-complicated internal flows. For flows at high Reynolds numbers, both an altered grid-generation procedure and a different formulation of the viscous terms are shown to be necessary. A hybrid Cartesian/body-fitted grid generation approach is demonstrated. In addition, a grid-generation procedure based on body-aligned cell cutting coupled with a viscous stensil-construction procedure based on quadratic programming is presented.

Coirier, William John↗
NASA NTRS1995

Adaptively Refined Euler and Navier-Stokes Solutions with a Cartesian-Cell Based Scheme

A Cartesian-cell based scheme with adaptive mesh refinement for solving the Euler and Navier-Stokes equations in two dimensions has been developed and tested. Grids about geometrically complicated bodies were generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells were created using polygon-clipping algorithms. The grid was stored in a binary-tree data structure which provided a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations were solved on the resulting grids using an upwind, finite-volume formulation. The inviscid fluxes were found in an upwinded manner using a linear reconstruction of the cell primitives, providing the input states to an approximate Riemann solver. The viscous fluxes were formed using a Green-Gauss type of reconstruction upon a co-volume surrounding the cell interface. Data at the vertices of this co-volume were found in a linearly K-exact manner, which ensured linear K-exactness of the gradients. Adaptively-refined solutions for the inviscid flow about a four-element airfoil (test case 3) were compared to theory. Laminar, adaptively-refined solutions were compared to accepted computational, experimental and theoretical results.

Coirier, William J.↗
NASA NTRS2005

Controlling Reflections from Mesh Refinement Interfaces in Numerical Relativity

A leading approach to improving the accuracy on numerical relativity simulations of black hole systems is through fixed or adaptive mesh refinement techniques. We describe a generic numerical error which manifests as slowly converging, artificial reflections from refinement boundaries in a broad class of mesh-refinement implementations, potentially limiting the effectiveness of mesh- refinement techniques for some numerical relativity applications. We elucidate this numerical effect by presenting a model problem which exhibits the phenomenon, but which is simple enough that its numerical error can be understood analytically. Our analysis shows that the effect is caused by variations in finite differencing error generated across low and high resolution regions, and that its slow convergence is caused by the presence of dramatic speed differences among propagation modes typical of 3+1 relativity. Lastly, we resolve the problem, presenting a class of finite-differencing stencil modifications which eliminate this pathology in both our model problem and in numerical relativity examples.

Baker, John G.↗
NASA NTRS2010

Interlaminar Stresses by Refined Beam Theories and the Sinc Method Based on Interpolation of Highest Derivative

Computation of interlaminar stresses from the higher-order shear and normal deformable beam theory and the refined zigzag theory was performed using the Sinc method based on Interpolation of Highest Derivative. The Sinc method based on Interpolation of Highest Derivative was proposed as an efficient method for determining through-the-thickness variations of interlaminar stresses from one- and two-dimensional analysis by integration of the equilibrium equations of three-dimensional elasticity. However, the use of traditional equivalent single layer theories often results in inaccuracies near the boundaries and when the lamina have extremely large differences in material properties. Interlaminar stresses in symmetric cross-ply laminated beams were obtained by solving the higher-order shear and normal deformable beam theory and the refined zigzag theory with the Sinc method based on Interpolation of Highest Derivative. Interlaminar stresses and bending stresses from the present approach were compared with a detailed finite element solution obtained by ABAQUS/Standard. The results illustrate the ease with which the Sinc method based on Interpolation of Highest Derivative can be used to obtain the through-the-thickness distributions of interlaminar stresses from the beam theories. Moreover, the results indicate that the refined zigzag theory is a substantial improvement over the Timoshenko beam theory due to the piecewise continuous displacement field which more accurately represents interlaminar discontinuities in the strain field. The higher-order shear and normal deformable beam theory more accurately captures the interlaminar stresses at the ends of the beam because it allows transverse normal strain. However, the continuous nature of the displacement field requires a large number of monomial terms before the interlaminar stresses are computed as accurately as the refined zigzag theory.

Slemp, Wesley C. H.↗