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At least 1,729 records · Page 96

Impact of High Performance Computing on the Detailed Simulation of Subsurface Flow and Contaminant Transport Using eSTOMP - 16341

The ability to model subsurface processes at the field-scale is essential to site closure and remedial action decisions. Field-scale models often require high-performance computing to meet the computational demands associated with complex systems, model calibration, and uncertainty quantification. eSTOMP, a parallel version of STOMP, is an analytical tool that meets the need for investigating coupled processes in the subsurface involving regional multi-fluid flow and biogeochemistry. The scalability of eSTOMP makes it ideal for simulating contaminant and geochemical reactive transport when long run times result from execution of a serial code. To demonstrate the impact of high-performance computation on subsurface analyses, the application of eSTOMP is presented for two sites. The first site involves uranium surface complexation within a highly dynamic, variably saturated flow field. The use of this model in conjunction with continued field monitoring is expected to provide a rigorous basis for developing operational strategies for field remediation and for defining defensible remediation endpoints. The second site involves the long-term dissolution of low-level radioactive glass emplaced within a near-surface repository. The waste form release rate is evaluated by modeling the basic physical and chemical processes that are known to control the waste form dissolution behavior, including pH and composition of the fluid contacting the glass. Simulations demonstrate that glass dissolution rates vary both in time and as a function of position within the disposal system, and that a 'leach rate' or radionuclide release rate parameter can only be estimated after identifying these impacts in a dynamic system. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

An Integrated Approach to Scaling Task-Based Runtime Systems for Next Generation Engineering problems

The need to scale next-generation industrial engineering problems to the largest computational platforms presents unique challenges. Such problems may have complex coupled multi-physics models, as well as computationally and communication intensive algorithms not often seen in standard academic problems, while also needing high-demand I/O for analysis purposes. In such cases even codes with good existing scaling properties may need significant changes, addressed in a cross-cutting way to solve such problems at extreme scales. These challenges relate to system components that were not previously problematic on less complex problems and/or at smaller computational scales. This paper illustrates these challenges for Uintah, a highly scalable asynchronous many-task runtime system being applied to the modeling of a 1000 MWe ultra-supercritical coal boiler. In order to model this formidable, production engineering problem, not only was an integrated approach needed that built upon existing scalable components in areas such as complex stencil calculations and linear algebra, but the significant challenges of high demand I/O, complex task graphs, and infrastructure inefficiencies also had to be addressed. This integrated approach allowed this problem to run on 256K CPU cores on Mira, with good weak scaling to 512K CPU cores and similar strong scaling, except for radiation. The need for strong scaling of a new ray tracing-based radiation model required substantial Uintah infrastructure improvements before 119K CPU cores and 7.5K GPUs on Titan could be used, with scaling out to 256K CPU cores and 16K GPUs. The resulting code demonstrates not only excellent overall scalability but a significant improvement in overall performance for the full-scale, production boiler problem.

97 MATHEMATICS AND COMPUTING↗

WE-D-303-00: Computational Phantoms

Modern medical physics deals with complex problems such as 4D radiation therapy and imaging quality optimization. Such problems involve a large number of radiological parameters, and anatomical and physiological breathing patterns. A major challenge is how to develop, test, evaluate and compare various new imaging and treatment techniques, which often involves testing over a large range of radiological parameters as well as varying patient anatomies and motions. It would be extremely challenging, if not impossible, both ethically and practically, to test every combination of parameters and every task on every type of patient under clinical conditions. Computer-based simulation using computational phantoms offers a practical technique with which to evaluate, optimize, and compare imaging technologies and methods. Within simulation, the computerized phantom provides a virtual model of the patient’s anatomy and physiology. Imaging data can be generated from it as if it was a live patient using accurate models of the physics of the imaging and treatment process. With sophisticated simulation algorithms, it is possible to perform virtual experiments entirely on the computer. By serving as virtual patients, computational phantoms hold great promise in solving some of the most complex problems in modern medical physics. In this proposed symposium, we will present the history and recent developments of computational phantom models, share experiences in their application to advanced imaging and radiation applications, and discuss their promises and limitations. Learning Objectives: Understand the need and requirements of computational phantoms in medical physics research Discuss the developments and applications of computational phantoms Know the promises and limitations of computational phantoms in solving complex problems.

60 APPLIED LIFE SCIENCES↗

Preparation and Characterization of Inclusion Complexes of β-Cyclodextrin and Phenolics from Wheat Bran by Combination of Experimental and Computational Techniques

Bitterness often associated with whole wheat products may be related to phenolics in the bran. Cyclodextrins (CDs) are known to form inclusion complexes. The objective was to form inclusion complexes between β-CD and wheat phenolics. Pure phenolic acids (trans-ferulic acid (FA), caffeic acid (CA), and p-coumaric acid (CO)) and phenolic acids from wheat bran were used to investigate complex formation potential. Complexes were characterized by spectroscopy techniques, and a computational and molecular modeling study was carried out. The relative amount of complex formation between β-CD and wheat bran extract was CA > CO > FA. The phenolic compounds formed inclusion complexes with β-CDs by non-covalent bonds. The quantum-mechanical calculations supported the experimental results. The most stable complex was CO/β-CD complex. The ΔH value for CO/β-CD complex was -11.72 kcal/mol and was about 3 kcal/mol more stable than the other complexes. The QSPR model showed good correlation between binding energy and 1H NMR shift for the H5 signal. This research shows that phenolics and β-CD inclusion complexes could be utilized to improve the perception of whole meal food products since inclusion complexes have the potential to mask the bitter flavor and enhance the stability of the phenolics in wheat bran.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a procedure for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe{sup 3+}, He{sup +} and H{sup +}) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Query Optimization for Graph Analytics on Linked Data Using SPARQL

Triplestores that support query languages such as SPARQL are emerging as the preferred and scalable solution to represent data and meta-data as massive heterogeneous graphs using Semantic Web standards. With increasing adoption, the desire to conduct graph-theoretic mining and exploratory analysis has also increased. Addressing that desire, this paper presents a solution that is the marriage of Graph Theory and the Semantic Web. We present software that can analyze Linked Data using graph operations such as counting triangles, finding eccentricity, testing connectedness, and computing PageRank directly on triple stores via the SPARQL interface. We describe the process of optimizing performance of the SPARQL-based implementation of such popular graph algorithms by reducing the space-overhead, simplifying iterative complexity and removing redundant computations by understanding query plans. Our optimized approach shows significant performance gains on triplestores hosted on stand-alone workstations as well as hardware-optimized scalable supercomputers such as the Cray XMT.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Seven open problems in applied combinatorics

We present and discuss seven different open problems in applied combinatorics. Additionally, the application areas relevant to this compilation include quantum computing, algorithmic differentiation, topological data analysis, iterative methods, hypergraph cut algorithms, and power systems.

97 MATHEMATICS AND COMPUTING↗

Highly parallel structured adaptive mesh refinement using parallel language-based approaches

Adaptive mesh refinement (AMR) calculations carried out on structured meshes play an exceedingly important role in several areas of science and engineering. A strategy for using Fortran 90 in an object-oriented fashion is presented. This permits AMR applications to be expressed in terms of familiar abstractions that are natural to the process of solving AMR hierarchies. The OpenMP features that are useful for parallel processing of AMR hierarchies in a load balanced fashion on multiprocessors is described.

computational↗

3-D components of a biological neural network visualized in computer generated imagery. II - Macular neural network organization

Computer-assisted reconstructions of small parts of the macular neural network show how the nerve terminals and receptive fields are organized in 3-dimensional space. This biological neural network is anatomically organized for parallel distributed processing of information. Processing appears to be more complex than in computer-based neural network, because spatiotemporal factors figure into synaptic weighting. Serial reconstruction data show anatomical arrangements which suggest that (1) assemblies of cells analyze and distribute information with inbuilt redundancy, to improve reliability; (2) feedforward/feedback loops provide the capacity for presynaptic modulation of output during processing; (3) constrained randomness in connectivities contributes to adaptability; and (4) local variations in network complexity permit differing analyses of incoming signals to take place simultaneously. The last inference suggests that there may be segregation of information flow to central stations subserving particular functions.

Ross, Muriel D.↗

NSR&D FY17 Report: CartaBlanca Capability Enhancements

Over the last several years, particle technology in the CartaBlanca code has been matured and has been successfully applied to a wide variety of physical problems. It has been shown that the particle methods, especially Los Alamos's dual domain material point method, is capable of computing many problems involves complex physics, chemistries accompanied by large material deformations, where the traditional finite element or Eulerian method encounter significant difficulties. In FY17, the CartaBlanca code has been enhanced with physical models and numerical algorithms. We started out to compute penetration and HE safety problems. Most of the year we focused on the TEPLA model improvement testing against the sweeping wave experiment by Gray et al., because it was found that pore growth and material failure are essentially important for our tasks and needed to be understood for modeling the penetration and the can experiments efficiently. We extended the TEPLA mode from the point view of ensemble phase average to include the effects of nite deformation. It is shown that the assumed pore growth model in TEPLA is actually an exact result from the theory. Alone this line, we then generalized the model to include finite deformations to consider nonlinear dynamics of large deformation. The interaction between the HE product gas and the solid metal is based on the multi-velocity formation. Our preliminary numerical results suggest good agreement between the experiment and the numerical results, pending further verification. To improve the parallel processing capabilities of the CartaBlanca code, we are actively working with the Next Generation Code (NGC) project to rewrite selected packages using C++. This work is expected to continue in the following years. This effort also makes the particle technology developed with CartaBlanca project available to other part of the laboratory. Working with the NGC project and rewriting some parts of the code also given us an opportunity to improve our numerical implementations of the method and to take advantage of recently advances in the numerical methods, such as multiscale algorithms.

97 MATHEMATICS AND COMPUTING↗

Nonlinear structural analysis on distributed-memory computers

A computational strategy is presented for the nonlinear static and postbuckling analyses of large complex structures on massively parallel computers. The strategy is designed for distributed-memory, message-passing parallel computer systems. The key elements of the proposed strategy are: (1) a multiple-parameter reduced basis technique; (2) a nested dissection (or multilevel substructuring) ordering scheme; (3) parallel assembly of global matrices; and (4) a parallel sparse equation solver. The effectiveness of the strategy is assessed by applying it to thermo-mechanical postbuckling analyses of stiffened composite panels with cutouts, and nonlinear large-deflection analyses of HSCT models on Intel Paragon XP/S computers. The numerical studies presented demonstrate the advantages of nested dissection-based solvers over traditional skyline-based solvers on distributed memory machines.

Watson, Brian C.↗

A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer

The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.

Jespersen, Dennis C.↗

Iterative spectral method for solving electrostatic or magnetostatic problems in complex and evolving heterostructures

Electrostatic or magnetostatic problems involving complex heterogeneity are nontrivial for modeling and simulation. Most existing numerical methods focus on sharp interface models and the computational cost increases with increasing complexity of the geometry. Here we develop an iterative spectral method, the bound charge successive approximation algorithm, to solve electrostatic or magnetostatic heterogeneity problems in the context of diffuse-interface modeling. As tests and verifications, this algorithm is applied to calculation of the depolarization factor of an ellipsoid, and simulation of random dielectric mixtures and the dielectophoretic motion of multiple particles. The algorithm shows excellent efficiency and the computational cost mainly depends on the permittivity or permeability contrast in the whole system, regardless of the complexity of the geometry. Specifically, for evolving heterostructures the solution of bound charge in one time step can be used as input for the next, which could further significantly shorten the iteration (approximation) process, making it practical to simulate the long-range electrostatic or magnetostatic interaction in complex and evolving heterostructures.

97 MATHEMATICS AND COMPUTING↗

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecular geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.

60 APPLIED LIFE SCIENCES↗

Scattering and Absorption Properties of Polydisperse Wavelength-sized Particles Covered with Much Smaller Grains

Using the results of direct, numerically exact computer solutions of the Maxwell equations, we analyze scattering and absorption characteristics of polydisperse compound particles in the form of wavelength-sized spheres covered with a large number of much smaller spherical grains.The results pertain to the complex refractive indices1.55 + i0.0003,1.55 + i0.3, and 3 + i0.1. We show that the optical effects of dusting wavelength-sized hosts by microscopic grains can vary depending on the number and size of the grains as well as on the complex refractive index. Our computations also demonstrate the high efficiency of the new superposition T-matrix code developed for use on distributed memory computer clusters.

Dlugach, Jana M.↗

Identification and Study of Validation Level Test Cases for Computational Modeling of Non-Charring Ablators

Computational modeling of Thermal Protection System (TPS) materials, used for aerospace applications, provides numerous advantages in preliminary selection and design of a heatshield material and shape for atmospheric entry vehicles. However, to serve as a reliable tool for prediction of material thermal and ablative behavior, the modeling approach needs to be validated against real experimental and flight data, preferably at a range of applied conditions. The validation study is typically very complex as it requires reliable measured data not only for the material thermal response and surface recession, but also well characterized environmental conditions. The validation problem becomes even more complex when the material thermal response is dictated by multi-physics effects such as solid conduction, in-depth thermal decomposition, pyrolysis gas flow and chemical reactions. The multi-physics effects complicate not only the modeling effort, but also the experimental measurement for validation of various aspects of the highly coupled problem. In this study, an attempt is made to identify suitable experimental data that could serve as a source for validation of material thermal response modeling tools. To reduce the computational complexity, this study focuses only on non-charring ablators, where the material thermal response could be modeled with a single governing equation for solid conduction and the ablation is limited only to the surface of the material. With a well characterized and publicly available experimental data being sparse, the study is limited in presenting test cases for only three materials: camphor, graphite and FiberForm® in the sequence of increased modeling complexity. Graphite is a commonly used TPS material for aerospace applications, both for leading edges of high-speed vehicles and internal insulation of solid rocket motors. FiberForm® is a porous carbon pre-form used in preparation of the well known PICA material Tran et al. [1996]. Inclusion of camphor into the list is conditioned with the relative simplicity in modeling the material thermal and chemical response and the low-enthalpy flow environment. In addition, camphor has been used as a simple test material for study of flow transition behavior by Stock and Ginoux [1973] and assessment of a heatshield shape change at flight relevant conditions by Rotondi et al. [2022]. In this work, the identified experimental data was extracted from the public literature and test cases that yet have been published. As it was found from the review, not a single test case contains an exhaustive set of data that would validate every aspect of the material physics. However, in the data collected, various aspects of the material behavior can be still validated, such as surface and in-depth temperature, amount of recession and a shape change. The identified experimental data for each case is accompanied with a characterized flow environment and simulated boundary conditions predicted by a Data-Parallel Line Relaxation (DPLR) code Wright et al. [1998]. In addition, material thermal response numerical simulations in each test case are performed with Kentucky Aerothermodynamics and Thermal Response System (KATS-MR) Zibitsker et al. [2022] providing a comparative study and a sanity check for the proposed validation data. Sample results from the performed numerical study are shown below. Figure 1 shows distribution of surface heat flux and pressure values on a hemi-cylinder model made of FiberForm® and tested in HyMETS arc-jet facility. The results are shown for the high pressure condition among the two tests. Flow simulation was performed with DPLR code on a quarter of original geometry. In the figure, the quarter shape was mirrored across zx and xy planes to show the complete distribution. Figure 2 shows the material response results for the high pressure case (7500 Pa), simulated with KATS-MR and a comparison to the experimental data for the surface temperature and shape shape. The simulation was performed on a 2-D slice, extracted in the xy plane at the middle of the sample. Figure 3 shows the material response simulation for the low pressure case (3500 Pa) and a comparison to the experimental data for surface temperature and shape change.

ablation↗

Predicting Unreinforced Fabric Mechanical Behavior with Recurrent Neural Networks

Unreinforced woven fabrics are widely employed in various high-performance applications, including parachute deployment systems, airbags, and ballistic armor. The analysis of such materials is inherently complex due to the multiscale structure of these materials, and the dependence of macroscale behavior on changes that occur at lower scales. Previously, NASA’s Multiscale Analysis Tool (NASMAT) showed its capability in predicting unreinforced fabric behavior at the macroscale by capturing finite rotations that occur at the mesoscale. Though effective, the tool can face high computational cost for large, complex problems, motivating the need for the development of a surrogate model that can capture the same behavior. A recurrent neural network (RNN) was developed and trained on virtual NASMAT data to mimic the physics-based solutions while improving the computational runtime. The architecture of the RNN to best simulate the fabric behavior was carefully crafted based on heuristic knowledge of predicting physics-based temporal data, manual hyperparameter case studies, and Hyperband optimization.. The resultant model was able to predict a variety of stress-strain curves for fabrics with different mesoscale geometries, and was further validated by comparing to experimental data for the K706 style Kevlar plain-weave fabric, demonstrating the ability of the model to effectively capture the geometric changes in the fabric without explicitly calculating them, as is done in NASMAT. Furthermore, the tool showed its ability to improve on the runtime by a factor of 10 for fabric solutions compared to the multiscale tool, which would further enable the simulation of complex loading scenarios on unreinforced fabrics.

Fabric↗