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DOE OSTI2018

Simulation tools for atom probe tomography: A path for diagnosis and treatment of image degradation

The ideal picture of a near-perfect 3D microscope often presented regarding Atom Probe Tomography faces several issues. These issues degrade the metrological performance of the instrument and find their roots in the phenomena acting at the atomic to the mesoscopic level in the vicinity of the surface of a field emitter. From the field evaporation process at the atomic scale, to the macroscopic scale of the instrument, the path to model the imaging process and to develop more accurate and reliable reconstruction algorithms is not a single lane road. This paper focused on the numerical methods used to understand, treat, and potentially heal imaging issues commonly affecting the data in atom probe experiments. A lot of room for improvement exists in solving accuracy problems observed in complex materials by means of purely electrostatic models describing the image formation in a classical approach. Looking at the sample at the atomic scale, the phenomena perturbing the imaging process are subtle. An examination of atomic scale modifications of the sample surface in the presence of a high surface electric field is therefore mandatory. Atomic scale molecular dynamic models integrating the influence of the high surface electric are being developed with this aim. It is also demonstrated that the complex behavior of atoms and molecules in high fields, and consequences on collected data, can be understood through the use of accurate ab-initio models modified to include the impact of the extreme surface electric field.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

NASA NTRS2018

GMI-IPS: Processing & Visualization Software Used in ATom DC-8 Aircraft Studies

NASA's Atmospheric Tomography Mission (ATom) deployed in each of the four seasons during 2016-2018, the DC-8 aircraft in order to establish global-scale datasets intended to improve the representation of chemically reactive gases in global atmospheric chemistry models (ACMs). The Global Modeling Initiative (GMI) executed simulations for each ATom flight using the GMI Chemistry Transport Model (GMI-CTM) to provide species concentrations of chemical gases along the DC-8 flight transects. To solve the problem of translating the GMI-CTM simulation data to the unique spatial resolutions of each ATom flight, the GMI ICARTT Processing Software (GMI-IPS) was developed.The GMI-IPS is written in Python and provides data processing, flight extraction, and visualization support for aircraft research projects using ICARTT format, which is a standard format for airborne instrument data. Additionally, the GMI-IPS interpolates global gridded model data from Hierarchical Data Format (HDF) to ICARTT compatible flight transects. Software classes for instruments and collections provided by the ATom DC-8 aircraft such as MER10, MMS, etc. are derived from a common base class. Other functionality provided by the GMI-IPS are: deriving missing flight entries along a transect, reading ICARTT entries from file, and providing Python data structures for storing flight and model information, and more.The GMI-IPS is GIT source controlled, has approximately 30,000 lines of code, and supports parallelization across data collections. It delivered GMI-CTM data for more than forty distinct DC-8 aircraft flights that took place under ATom. The output ICARTT files adhere to format standard V1.1, and pass the scan utility provided by NASA LaRC Airborne Science Data for Atmospheric Composition. This presentation will include a software and methods overview, and results from ATom, including assessments using the GMI-CTM showing how well observations from ATom flight transects represent a broader region.

Damon, M. R.↗

DOE OSTI2024

tomoCAM : fast model-based iterative reconstruction via GPU acceleration and non-uniform fast Fourier transforms

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM , is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter -based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2014

Validation of Spherically Symmetric Inversion by Use of a Tomographically Reconstructed Three-Dimensional Electron Density of the Solar Corona

Determining the coronal electron density by the inversion of white-light polarized brightness (pB) measurements by coronagraphs is a classic problem in solar physics. An inversion technique based on the spherically symmetric geometry (spherically symmetric inversion, SSI) was developed in the 1950s and has been widely applied to interpret various observations. However, to date there is no study of the uncertainty estimation of this method. We here present the detailed assessment of this method using a three-dimensional (3D) electron density in the corona from 1.5 to 4 solar radius as a model, which is reconstructed by a tomography method from STEREO/COR1 observations during the solar minimum in February 2008 (Carrington Rotation, CR 2066).We first show in theory and observation that the spherically symmetric polynomial approximation (SSPA) method and the Van de Hulst inversion technique are equivalent. Then we assess the SSPA method using synthesized pB images from the 3D density model, and find that the SSPA density values are close to the model inputs for the streamer core near the plane of the sky (POS) with differences generally smaller than about a factor of two; the former has the lower peak but extends more in both longitudinal and latitudinal directions than the latter. We estimate that the SSPA method may resolve the coronal density structure near the POS with angular resolution in longitude of about 50 deg. Our results confirm the suggestion that the SSI method is applicable to the solar minimum streamer (belt), as stated in some previous studies. In addition, we demonstrate that the SSPA method can be used to reconstruct the 3D coronal density, roughly in agreement with the reconstruction by tomography for a period of low solar activity (CR 2066). We suggest that the SSI method is complementary to the 3D tomographic technique in some cases, given that the development of the latter is still an ongoing research effort.

corona↗

DOE OSTI2018

Verification of Spent Nuclear Fuel in Sealed Dry Storage Casks via Measurements of Cosmic-Ray Muon Scattering

Most of the plutonium in the world resides inside spent nuclear reactor fuel rods. This high-level radioactive waste is commonly held in long-term storage within large, heavily shielded casks. Currently, international nuclear safeguards inspectors have no stand-alone method of verifying the amount of reactor fuel stored within a sealed cask. In this paper, we demonstrate experimentally that measurements of the scattering angles of cosmic-ray muons, which pass through a storage cask, can be used to determine if spent fuel assemblies are missing without opening the cask. Finally, this application of technology and methods commonly used in high-energy particle physics provides a potential solution to this long-standing problem in international nuclear safeguards.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Benchmarking Quantum Processor Performance through Quantum Distance Metrics Over An Algorithm Suite

Quantum computing is poised to solve computational paradigms that classical computing could never feasibly reach. Tasks such as prime factorization to Quantum Chemistry are examples of classically difficult problems that have analogous algorithms that are sped up on quantum computers. To attain this computational advantage, we must first traverse the noisy intermediate scale quantum (NISQ) era, in which quantum processors suffer from compounding noise factors that can lead to unreliable algorithm induction producing noisy results. We describe QASMBench, a suite of QASM-level (Quantum assembly language) benchmarks that challenge all realisable angles of quantum processor noise. We evaluate a large portion of these algorithms by performing density matrix tomography on 14 IBMQ Quantum devices.

Stein, Samuel A.↗

DOE OSTI2021

Imposing equilibrium on experimental 3-D stress fields using Hodge decomposition and FFT-based optimization

Here, we present a methodology to impose micromechanical constraints, i.e. stress equilibrium at grain and sub-grain scale, to an arbitrary (non-equilibrated) voxelized stress field obtained, for example, by means of synchrotron X-ray diffraction techniques. The method consists in finding the equilibrated stress field closest (in L 2 -norm sense) to the measured non-equilibrated stress field, via the solution of an optimization problem. The extraction of the divergence-free (equilibrated) part of a general (non-equilibrated) field is performed using the Hodge decomposition of a symmetric matrix field, which is the generalization of the Helmholtz decomposition of a vector field into the sum of an irrotational field and a solenoidal field. The combination of: a) the Euler–Lagrange equations that solve the optimization problem, and b) the Hodge decomposition, gives a differential expression that contains the bi-harmonic operator and two times the curl operator acting on the experimental stress field. These high-order derivatives can be efficiently performed in Fourier space. The method is applied to filter the non-equilibrated parts of a synthetic piecewise constant stress fields with a known ground truth, and stress fields in Gum Metal, a beta-Ti-based alloy measured in-situ using Diffraction Contrast Tomography (DCT). In both cases, the largest corrections were obtained near grain boundaries.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Self-supervised physics-informed generative networks for phase retrieval from a single X-ray hologram

X-ray phase contrast imaging significantly improves the visualization of structures with weak or uniform absorption, broadening its applications across a wide range of scientific disciplines. Propagation-based phase contrast is particularly suitable for time- or dose-critical in vivo/in situ/operando (tomography) experiments because it requires only a single intensity measurement. However, the phase information of the wave field is lost during the measurement and must be recovered. Conventional algebraic and iterative methods often rely on specific approximations or boundary conditions that may not be met by many samples or experimental setups. In addition, they require manual tuning of reconstruction parameters by experts, making them less adaptable for complex or variable conditions. Here we present a self-learning approach for solving the inverse problem of phase retrieval in the near-field regime of Fresnel theory using a single intensity measurement (hologram). A physics-informed generative adversarial network is employed to reconstruct both the phase and absorbance of the unpropagated wave field in the sample plane from a single hologram. Unlike most state-of-the-art deep learning approaches for phase retrieval, our approach does not require paired, unpaired, or simulated training data. This significantly broadens the applicability of our approach, as acquiring or generating suitable training data remains a major challenge due to the wide variability in sample types and experimental configurations. The algorithm demonstrates robust and consistent performance across diverse imaging conditions and sample types, delivering quantitative, high-quality reconstructions for both simulated data and experimental datasets acquired at beamline P05 at PETRA III (DESY, Hamburg), operated by Helmholtz-Zentrum Hereon. Furthermore, it enables the simultaneous retrieval of both phase and absorption information.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Geometric state function for two-fluid flow in porous media

Models that describe two-fluid flow in porous media suffer from a widely recognized problem that the constitutive relationships used to predict capillary pressure as a function of the fluid saturation are nonunique, thus requiring a hysteretic description. As an alternative to the traditional perspective, we consider a geometric description of the capillary pressure, which relates the average mean curvature, the fluid saturation, the interfacial area between fluids, and the Euler characteristic. The state equation is formulated using notions from algebraic topology and cast in terms of measures of the macroscale state. Synchrotron-based x-ray microcomputed tomography and high-resolution pore-scale simulation is applied to examine the uniqueness of the proposed relationship for six different porous media. We show that the geometric state function is able to characterize the microscopic fluid configurations that result from a wide range of simulated flow conditions in an averaged sense. The geometric state function can serve as a closure relationship within macroscale models to effectively remove hysteretic behavior attributed to the arrangement of fluids within a porous medium. As a result, this provides a critical missing component needed to enable a new generation of higher fidelity models to describe two-fluid flow in porous media.

42 ENGINEERING↗

DOE OSTI2019

Evolution of damage and failure in an additively manufactured 316L SS structure: experimental reinvestigation of the third Sandia fracture challenge

The third Sandia Fracture Challenge (SFC3) was a benchmark problem for comparing experimental and simulated ductile deformation and failure in an additively manufactured (AM) 316L stainless steel structure. One surprising observation from the SFC3 was the Challenge-geometry specimens had low variability in global load versus displacement behavior, attributed to the large stress-concentrating geometric features dominating the global behavior, rather than the AM voids that tend to significantly influence geometries with uniform cross-sections. This current study reinvestigates the damage and failure evolution of the Challenge-geometry specimens, utilizing interrupted tensile testing with micro-computed tomography (micro-CT) scans to monitor AM void and crack growth from a virgin state through complete failure. This study did not find a correlation between global load versus displacement behavior and AM void attributes, such as void volume, location, quantity, and relative size, which incidentally corroborates the observation from the SFC3. However, this study does show that the voids affect the local behavior of damage and failure. Surface defects (i.e. large voids located on the surface, far exceeding the nominal surface roughness) that were near the primary stress concentration affected the location of crack initiation in some cases, but they did not noticeably affect the global response. The fracture surfaces were a combination of classic ductile dimples and crack deviation from a more direct path favoring intersection with AM voids. Even though the AM voids promoted crack deviation, pre-test micro-CT scan statistics of the voids did not allow for conclusive predictions of preferred crack paths. This study is a first step towards investigating the importance of voids on the ductile failure of AM structures with stress concentrations.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Relaxation algorithms for matrix completion, with applications to seismic travel-time data interpolation

Travel time tomography is used to infer the underlying three-dimensional wavespeed structure of the Earth by fitting seismic travel time data collected at surface stations. Data interpolation and denoising techniques are important pre-processing steps that use prior knowledge about the data, including parsimony in the frequency and wavelet domains, low-rank structure of matricizations, and local smoothness. In this work, we show how local smoothness structure can be combined with low rank constraints using level-set optimization formulations, and develop a new relaxation algorithm that can efficiently solve these joint problems. In the seismology setting, we use the approach to interpolate missing stations and de-noise observed stations. The new approach is competitive with alternative algorithms, and offers new functionality to interpolate observed data using both smoothness and low rank structure in the presence of data fitting constraints.

constrained optimization↗

DOE OSTI2023

Predictive Modeling of Electrodeposition in a Single Pore Flow-Through Electrode: From Electronucleation to Coating Thickness Uniformity

The emergence of advanced manufacturing methods capable of producing porous three-dimensional structures has expanded the design space for next-generation functional components. The ability to fabricate ordered 3D foams for use in electrocatalysis reactors has increased the need for controlled deposition of catalytic metals onto porous support materials, such as carbon. However, there is a lack of clear design guidelines for electrodeposition onto 3D substrates, due to the geometric complexity and multi-scale nature of the problem. Furthermore, electro-nucleation phenomena are often overlooked in macro-scale models of current distribution during deposition. Here, a graphite flow-through electrode (FTE) is used as a model system for copper deposition within a single pore. Potential distributions and electro-nucleation phenomena are coupled in a continuum level model by incorporating nucleation size and density as a function of overpotential, determined experimentally using in situ atomic force microscopy (AFM). The model predictions are validated by measuring the coating uniformity in the pore using micro-computed X-ray tomography (μCT). A scaling analysis comprising dimensionless parameters such as the Wagner number is presented. The simplified scaling relationship framework can guide the electrodeposition process and electrode design to optimize plating of porous substrates under fluid flow conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Crustal Scale Travel Time Prediction with the SALSA3D Framework and Machine Learning

The SALSA3D project aims to improve our models used in travel time prediction. The current version uses tomographic modeling for propagation through the Earth’s mantle because of the large number (order of millions) of observations of seismic phases which primarily traverse the Earth’s mantle and the ability to pose the travel time problem as a set of linear equations. However, all seismic rays traverse the crust to reach receivers at the surface and therefore models of propagation through the crust are required. Therefore, the primary motivation for this study is to explore how to increase the scope of the SALSA3D project to phases which travel primarily through the crust. In this report, we evaluate new, machine learning based and physics-based methods to model these travel times for integration into the SALSA3D framework. Our results suggest that using our existing physics-based travel time tomography method is a viable approach for the regional to global scale, but better predictive capabilities can be achieved through a neural network trained on the region of interest for near-regional offsets. We suggest future iterations of SALSA3D should incorporate machine learning tools such as Physics-Informed Neural Networks or Bayesian Neural Networks.

58 GEOSCIENCES↗

DOE OSTI2023

Shedding light on shadow generalized parton distributions

The feasibility of extracting generalized parton distributions (GPDs) from deeply virtual Compton scattering (DVCS) data has recently been questioned because of the existence of an infinite set of so-called “shadow GPDs” (SGPDs). These SGPDs depend on the process and manifest as multiple solutions (at a fixed scale 𝑄 2 ) to the inverse problem that needs to be solved to infer GPDs from DVCS data. SGPDs therefore pose a significant challenge for extracting GPDs from DVCS data. With this motivation we study the extent to which QCD evolution can provide constraints on SGPDs. This is possible because the known classes of SGPDs begin to contribute to observables after evolution, and can then be constrained (at the input scale 𝑄$^{2}_{0}$) by data that has a finite 𝑄 2 range. The impact that SGPDs could have on determining the total angular momentum, pressure and sheer force distributions, and tomography is also discussed. We find that 𝑄 2 evolution, given empirical data over a wide range of skewness (𝜉 ) and 𝑄 2 scales, constrains the SGPDs studied at low 𝑥 and low 𝜉. If this finding generalizes to all SGPDs—and we have not been able to find any SGPDs with qualitatively different behavior—then this potentially makes extraction of GPDs from DVCS possible over a limited range of 𝑥 and 𝜉.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

mesoflow [SWR-22-56]

Mesoflow is a continuum scale simulation tool developed specifically for modeling transport and chemistry at the mesoscale. Our solver utilizes Cartesian block-structured adaptive mesh refinement to resolve complex surface morphologies (of catalysts/biomass particles among others) directly obtained from X-ray tomography data. An immersed boundary based formulation enables rapid representation of complex geometries prevalent in most mesoporous interfaces. The solver is developed on top of open-source performance portable library, AMReX, providing parallel execution capabilities on current and upcoming high-performance-computing (HPC) architectures. Our flexible software framework enables integration of complex chemical mechanisms at heterogenous interfaces and time-split algorithms for circumventing highly disparate reaction and flow time-scales. Our current studies indicate a ten-fold performance gain by using graphics-processing-units (GPU) compared to a single processor for representative problem sizes (2 million cell mesh).

Sitaraman, Hariswaran↗

DOE OSTI2022

Mesoflow: An Open-Source Reacting Flow Solver for Catalysis at Mesoscale

We present the capabilities and software performance metrics of our open-source continuum solver for catalysis, Mesoflow, developed specifically for modeling transport and chemistry at the mesoscale. Our solver utilizes Cartesian block-structured adaptive mesh refinement to resolve complex catalyst surface morphologies directly obtained from X-ray tomography data. An immersed boundary based formulation enables rapid representation of complex geometries prevalent in most mesoporous catalyst interfaces. The solver is developed on top of open-source performance portable library, AMReX, providing parallel execution capabilities on current and upcoming high-performance-computing (HPC) architectures. Our flexible software framework enables integration of complex chemical mechanisms at heterogenous interfaces and time-split algorithms for circumventing highly disparate reaction and flow time-scales. Our current studies indicate a ten-fold performance gain by using graphics-processing-units (GPUs) compared to a single processor for representative problem sizes (2 million cell mesh). We will also present a brief introduction on how to build and use this software for application problems pertaining to catalytic upgrading and gas transport within porous catalyst particles.

adaptive meshing↗

DOE OSTI2023

A state-of-the-art review of experimental and computational studies of granular materials: Properties, advances, challenges, and future directions

Modeling of heterogeneous materials and media is a problem of fundamental importance to a wide class of phenomena and systems, ranging from condensed matter physics, soft materials, and composite media to porous media, biological systems, geosystems, ceramic engineering, pharmaceutical science and even in space discoveries. Among the most important materials are granular systems, which have received intense interest from the engineering, physics, and mathematics communities. In this review paper, the recent developments and new advances in experimental, and computational methods on a variety of scales and physics that extend understanding to a wide range of materials and phenomena are reviewed. Experimental advances include computed neutron and nanometer-scale tomography, magnetic resonance imaging, refractive index matching, digital image correlation, acoustic emission analysis, and the most recent 4D techniques. Furthermore, a tremendous shift has occurred from the continuum scale to micro-scale and developing multiscale approaches. As such, various computational methods, including, constitutive modeling, discrete modeling, and multiscale approaches, have been developed. In conclusion, aside from all these evolutions, more complicated modeling called coupled, or multiphysics, systems representing a simultaneous presence of heat, fluid, chemical variation, and mechanical effect are also explored.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Quantum circuit fidelity estimation using machine learning

The computational power of real-world quantum computers is limited by errors. When using quantum computers to perform algorithms which cannot be efficiently simulated classically, it is important to quantify the accuracy with which the computation has been performed. In this work, we introduce a machine learning-based technique to estimate the fidelity between the state produced by a noisy quantum circuit and the target state corresponding to ideal noise-free computation. Our machine learning model is trained in a supervised manner, using smaller or simpler circuits for which the fidelity can be estimated using other techniques like direct fidelity estimation and quantum state tomography. Here we demonstrate that, for simulated random quantum circuits with a realistic noise model, the trained model can predict the fidelities of more complicated circuits for which such methods are infeasible. In particular, we show that the trained model may make predictions for circuits with higher degrees of entanglement than were available in the training set and that the model may make predictions for non-Clifford circuits even when the training set included only Clifford-reducible circuits. This empirical demonstration suggests classical machine learning may be useful for making predictions about beyond-classical quantum circuits for some non-trivial problems.

97 MATHEMATICS AND COMPUTING↗