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This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science.
This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics. fluid mechanics, and computer science during the period April 1, 1999 through September 30. 1999.
The Center for Tokamak Transients Simulations (CTTS) consists of computational plasma physicists, computer scientists, and applied mathematicians who are together developing and applying simulation software to improve our understanding of and ability to predict and control transient events in tokamak discharges, particularly those that lead to violent disruptions. We have major simulation activities concerning disruptions that are caused by violating ideal MHD stability criteria, vertical displacement events, resistive wall modes, and tearing modes. We are performing comprehensive modeling of disruption mitigation techniques, particularly by shattered pellet injection (SPI). The Center is built around two mature extended MHD codes: NIMROD and M3D-C1. These codes are being extended in a number of ways as required by the demands of disruption modeling, and are being optimized to work well for larger problem size and modern computer architectures as required to model tokamak plasmas with realistic parameters over the required timescales. The codes will be coupled to the FronTier code for state-of-the-art modeling of SPI. Validation with experimental data on DIII-D, NSTX, and JET is being facilitated by rigorous uncertainty quantification (UQ). The high-level objectives of the center are to: (1) Develop better understanding and improved predictive capability of when crossing a linear stability boundary will likely lead to a disruption, (2) Provide a tool for calculating vessel forces, both axisymmetric and non-axisymmetric, for worst case VDE and other disruptions in tokamaks, (3) Develop increased understanding and improved predictive capability for locked mode disruptions and how best to avoid them, (4) Develop, verify, and validate 3D models for disruption mitigation by shattered pellets that can be used to design and optimize a system for future tokamaks, and (5) Increase the efficiency and scalability of the M3D-C1 and NIMROD codes so that they can model disruptions in ITER scale devices using the most powerful DOE HPC hardware, and (6) Demonstrate code-coupling via FronTier coupling with NIMROD and M3D-C1 and by interfacing these codes within a WDM framework.
A practical method of data assimilation for use with large, nonlinear, ocean general circulation models is explored. A Kalman filter based on approximation of the state error covariance matrix is presented, employing a reduction of the effective model dimension, the error's asymptotic steady state limit, and a time-invariant linearization of the dynamic model for the error integration. The approximations lead to dramatic computational savings in applying estimation theory to large complex systems. We examine the utility of the approximate filter in assimilating different measurement types using a twin experiment of an idealized Gulf Stream. A nonlinear primitive equation model of an unstable east-west jet is studied with a state dimension exceeding 170,000 elements. Assimilation of various pseudomeasurements are examined, including velocity, density, and volume transport at localized arrays and realistic distributions of satellite altimetry and acoustic tomography observations. Results are compared in terms of their effects on the accuracies of the estimation. The approximate filter is shown to outperform an empirical nudging scheme used in a previous study. The examples demonstrate that useful approximate estimation errors can be computed in a practical manner for general circulation models.
A practical method of data assimilation for use with large, nonlinear, ocean general circulation models is explored. A Kalman filter based on approximations of the state error covariance matrix is presented, employing a reduction of the effective model dimension, the error's asymptotic steady-state limit, and a time-invariant linearization of the dynamic model for the error integration. The approximations lead to dramatic computational savings in applying estimation theory to large complex systems. We examine the utility of the approximate filter in assimilating different measurement types using a twin experiment of an idealized Gulf Stream. A nonlinear primitive equation model of an unstable east-west jet is studied with a state dimension exceeding 170,000 elements. Assimilation of various pseudo measurements is examined, including velocity, density, and volume transport at localized arrays, and realistic distributions of satellite altimetry and acoustic tomography observations. Results are compared in terms of their effects on the accuracies of the estimation. The approximate filter is shown to outperform a previous study that used an empirical nudging scheme. The examples demonstrate that useful approximate estimation errors can be computed in a practical manner for general circulation models.
In this paper, we present a novel strategy for incorporating massive parallelism into the solution of Maxwell's equations using finite-difference time-domain methods. In a departure from previous techniques wherein spatial parallelism is used, our approach exploits massive temporal parallelism by computing all of the time steps in parallel.
Advanced computational procedures are applied to an improved model of solar wind flow past Venus to calculate the locations of the ionopause and bow wave and the properties of the flowing ionosheath plasma in the intervening region. The theoretical method is based on a single-fluid, steady, dissipationless, magneto-hydrodynamic continuum model and is appropriate for the calculation of axisymmetric supersonic, super-Alfvenic solar wind flow past a nonmagnetic planet possessing a sufficiently dense ionosphere to stand off the flowing plasma above the subsolar point and elsewhere. Determination of time histories of plasma and magnetic field properties along an arbitrary spacecraft trajectory and provision for an arbitrary oncoming direction of the interplanetary solar wind have been incorporated in the model. An outline is provided of the underlying theory and computational procedures, and sample comparisons of the results are presented with observations from the Pioneer Venus orbiter.
Rotorcraft operating in high-threat environments fly close to the earth's surface to utilize surrounding terrain, vegetation, or manmade objects to minimize the risk of being detected by an enemy. Increasing levels of concealment are achieved by adopting different tactics during low-altitude flight. Rotorcraft employ three tactics during low-altitude flight: low-level, contour, and nap-of-the-earth (NOE). The key feature distinguishing the NOE mode from the other two modes is that the whole rotorcraft, including the main rotor, is below tree-top whenever possible. This leads to the use of lateral maneuvers for avoiding obstacles, which in fact constitutes the means for concealment. The piloting of the rotorcraft is at best a very demanding task and the pilot will need help from onboard automation tools in order to devote more time to mission-related activities. The development of an automation tool which has the potential to detect obstacles in the rotorcraft flight path, warn the crew, and interact with the guidance system to avoid detected obstacles, presents challenging problems. Research is described which applies techniques from computer vision to automation of rotorcraft navigtion. The effort emphasizes the development of a methodology for detecting the ranges to obstacles in the region of interest based on the maximum utilization of passive sensors. The range map derived from the obstacle-detection approach can be used as obstacle data for the obstacle avoidance in an automatic guidance system and as advisory display to the pilot. The lack of suitable flight imagery data presents a problem in the verification of concepts for obstacle detection. This problem is being addressed by the development of an adequate flight database and by preprocessing of currently available flight imagery. The presentation concludes with some comments on future work and how research in this area relates to the guidance of other autonomous vehicles.
We introduce a new low-dimensional model of high-dimensional numerical simulation data based on low-rank tensor decompositions. Our new model aims to minimize differences between the model data and simulation data as well as functions of the model data and functions of the simulation data. This novel approach to dimensionality reduction of simulation data provides a means of directly incorporating quantities of interests and invariants associated with conservation principles associated with the simulation data into the low-dimensional model, thus enabling more accurate analysis of the simulation without requiring access to the full set of high-dimensional data. Computational results of applying this approach to two standard low-rank tensor decompositions of data arising from simulation of combustion and plasma physics are presented.
Uncertainty quantification (UQ) plays a pivotal role in scientific machine learning, especially when surrogate models are used to approximate complex systems. Although multilayer perceptions (MLPs) are commonly employed as surrogates, they often suffer from overfitting due to their large number of parameters. Kolmogorov-Arnold networks (KANs) offer an alternative solution with fewer parameters. However, gradient-based inference methods, such as Hamiltonian Monte Carlo (HMC), may result in computational inefficiency when applied to KANs, especially for large-scale datasets, due to the high cost of back-propagation. To address these challenges, we propose a novel approach, combining the dropout Tikhonov ensemble Kalman inversion (DTEKI) with Chebyshev KANs. This gradient-free method effectively mitigates overfitting and enhances numerical stability. In addition, we incorporate the active subspace method to reduce the parameter-space dimensionality, allowing us to improve the accuracy of predictions and obtain more reliable uncertainty estimates. Extensive experiments demonstrate the efficacy of our approach in various test cases, including scenarios with large datasets and high noise levels. Our results show that the new method achieves comparable or better accuracy, much higher efficiency as well as stability compared to HMC, in addition to scalability. Moreover, by leveraging the low-dimensional parameter subspace, our method preserves prediction accuracy while substantially reducing further the computational cost.
Proper orthogonal decomposition (POD) is the mathematical basis of a method of constructing low-order mathematical models for the "gray-box" fault-detection algorithm that is a component of a diagnostic system known as beacon-based exception analysis for multi-missions (BEAM). POD has been successfully applied in reducing computational complexity by generating simple models that can be used for control and simulation for complex systems such as fluid flows. In the present application to BEAM, POD brings the same benefits to automated diagnosis. BEAM is a method of real-time or offline, automated diagnosis of a complex dynamic system.The gray-box approach makes it possible to utilize incomplete or approximate knowledge of the dynamics of the system that one seeks to diagnose. In the gray-box approach, a deterministic model of the system is used to filter a time series of system sensor data to remove the deterministic components of the time series from further examination. What is left after the filtering operation is a time series of residual quantities that represent the unknown (or at least unmodeled) aspects of the behavior of the system. Stochastic modeling techniques are then applied to the residual time series. The procedure for detecting abnormal behavior of the system then becomes one of looking for statistical differences between the residual time series and the predictions of the stochastic model.
The African swine fever virus (ASFV) is an often deadly disease in swine and poses a threat to swine livestock and swine producers. With its complex genome containing more than 150 coding regions, developing effective vaccines for this virus remains a challenge due to a lack of basic knowledge about viral protein function and protein–protein interactions between viral proteins and between viral and host proteins. In this work, we identified ASFV-ASFV protein–protein interactions (PPIs) using artificial intelligence-powered protein structure prediction tools. We benchmarked our PPI identification workflow on the Vaccinia virus, a widely studied nucleocytoplasmic large DNA virus, and found that it could identify gold-standard PPIs that have been validated in vitro in a genome-wide computational screening. We applied this workflow to more than 18,000 pairwise combinations of ASFV proteins and were able to identify seventeen novel PPIs, many of which have corroborating experimental or bioinformatic evidence for their protein–protein interactions, further validating their relevance. Two protein–protein interactions, I267L and I8L, I267L__I8L, and B175L and DP79L, B175L__DP79L, are novel PPIs involving viral proteins known to modulate host immune response.
Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, fluid mechanics including fluid dynamics, acoustics, and combustion, aerodynamics, and computer science during the period 1 Apr. 1992 - 30 Sep. 1992 is summarized.
Over the past few decades, computer-controlled optical surfacing (CCOS) systems have become more deterministic. A target surface profile can be predictably achieved with a combination of tools of different sizes. However, deciding the optimal set of tool sizes that will achieve the target residual error in the shortest run time is difficult, and no general guidance has been proposed in the literature. In this paper, we present a computer-assisted study on choosing the proper tool size for a given surface error map. First, we propose that the characteristic frequency ratio (CFR) can be used as a general measure of the correction capability of a tool over a surface map. Second, the performance of different CFRs is quantitatively studied with a computer simulation by applying them to guide the tool size selection for polishing a large number of randomly generated surface maps with similar initial spatial frequencies and root mean square errors. Finally, we find that CFR = 0.75 achieves the most stable trade-off between the total run time and the number of iterations and thus can be used as a general criterion in tool size selection for CCOS processes. To the best of our knowledge, the CFR is the first criterion that ties tool size selection to overall efficiency.
This workshop aims to identify key research directions for transforming biology using artificial intelligence (AI), machine learning (ML) and computational methods to facilitate the discovery of new behaviors, mechanisms, and designs of biological processes relevant to DOE missions, underpinning a broader U.S. bioeconomy. By developing novel AI/ML technologies to analyze and interpret complex biological data, researchers can organize and simulate biological processes at various scales as well as advance predictive understanding and manipulation of biological systems. This integration of computation, experimentation, and next-generation experimental technologies can lead to discoveries in new biological behaviors and mechanisms relevant to DOE missions. The focus is on how advanced computational and mathematical methods can impact this mission by exploring digital twins, foundation models, automated laboratory experiments, modeling of complex living systems, and data-driven approaches for the biodesign of plants and microbial systems. While data management is important, it is not the primary focus of this workshop, which will assess the current state, trends, and AI/ML challenges at the interface between biology and computational science to identify opportunities for high-impact research at their intersection. The goal is to define research needs and opportunities that align with biological sciences, computational sciences, and applied mathematics research.
This report describes the computational steps involved in executing a finite-element-based perturbation model for computing the rotor dynamic coefficients of a shrouded pump impeller or a simple seal. These arise from the fluid/rotor interaction in the clearance gap. In addition to the sample cases, the computational procedure also applies to a separate category of problems referred to as the 'seal-like' category. The problem, in this case, concerns a shrouded impeller, with the exception that the secondary, or leakage, passage is totally isolated from the primary-flow passage. The difference between this and the pump problem is that the former is analytically of the simple 'seal-like' configuration, with two (inlet and exit) flow-permeable stations, while the latter constitutes a double-entry / double-discharge flow problem. In all cases, the problem is that of a rotor clearance gap. The problem here is that of a rotor excitation in the form of a cylindrical whirl around the housing centerline for a smooth annular seal. In its centered operation mode, the rotor is assumed to give rise to an axisymmetric flow field in the clearance gap. As a result, problems involving longitudinal or helical grooves, in the rotor or housing surfaces, go beyond the code capabilities. Discarding, for the moment, the pre- and post-processing phases, the bulk of the computational procedure consists of two main steps. The first is aimed at producing the axisymmetric 'zeroth-order' flow solution in the given flow domain. Detailed description of this problem, including the flow-governing equations, turbulence closure, boundary conditions, and the finite-element formulation, was covered by Baskharone and Hensel. The second main step is where the perturbation model is implemented, with the input being the centered-rotor 'zeroth-order' flow solution and a prescribed whirl frequency ratio (whirl frequency divided by the impeller speed). The computational domain, in the latter case, is treated as three dimensional, with the number of computational planes in the circumferential direction being specified a priori. The reader is reminded that the deformations in the finite elements are all infinitesimally small because the rotor eccentricity itself is a virtual displacement. This explains why we have generically termed the perturbation model the 'virtually' deformable finite-element category. The primary outcome of implementing the perturbation model is the tangential and radial components, F(sub theta)(sup *) and F(sub r)(sup *) of the fluid-exerted force on the rotor surface due to the whirling motion. Repetitive execution of the perturbation model subprogram over a sufficient range of whirl frequency ratios, and subsequent interpolation of these fluid forces, using the least-square method, finally enable the user to compute the impeller rotor dynamic coefficients of the fluid/rotor interaction. These are the direct and cross-coupled stiffness, damping, and inertia effects of the fluid/rotor interaction.
Fan noise continues to be a significant issue for commercial aircraft engines and there still exists a requirement for improved understanding of the fundamental issues associated with fan noise source mechanisms. At the present time, most of the prediction methods identify the dominant acoustic sources to be associated with the stator vanes or blade trailing edges which are downstream of the fan face. However recent studies have shown that acoustic waves are significantly attenuated as they propagate upstream through a rotor, and if the appropriate corrections are applied, sound radiation from the engine inlet is significantly underpredicted. The prediction models can only be applied to fans with subsonic tip speeds. In contrast, most aircraft engines have fan tip speeds which are transonic and this implies an even higher attenuation for upstream propagating acoustic waves. Consequently understanding how sound propagates upstream through the fan is an important, and not well understood phenomena. The objective of this study is to provide improved insight into the upstream propagation effects through a rotor which are relevant to full scale engines. The focus of this study is on broadband fan noise generated by boundary layer turbulence interacting with the trailing edges of the fan blades. If this source mechanism is important upstream of the fan, the sound must propagate upstream through a transonic non uniform flow which includes large gradients and non linearities. Developing acoustic propagation models in this type of flow is challenging and currently limited to low frequency applications, where the frequency is of the same order as the blade passing frequency of the fan. For trailing edge noise, much higher frequencies are relevant and so a suitable approach needs to be developed, which is not limited by an unacceptably large computational effort. In this study we are in the process of developing a computational method which applies for the high frequencies of interest, and allows for any type of flow field associated with the fan. In this progress report the approach to be used and the basic equations will be presented. Some initial results will be given, but these are preliminary and need further verification.
Approximate computing techniques, which trade off the computation accuracy of an algorithm for better performance and energy efficiency, have been successful in reducing computation and power costs in several domains. However, error sensitive applications in high-performance computing are unable to benefit from existing approximate computing strategies that are not developed with guaranteed error bounds. While approximate computing techniques can be developed for individual high-performance computing applications by domain specialists, this often requires additional theoretical analysis and potentially extensive software modification. Hence, the development of low-level error-bounded approximate computing strategies that can be introduced into any high-performance computing application without requiring additional analysis or significant software alterations is desirable. In this paper, we provide a contribution in this direction by proposing a general framework for designing error-bounded approximate computing strategies and apply it to the dot product kernel to develop \bf qdot---an error-bounded approximate dot product kernel. Following the introduction of qdot, here we perform a theoretical analysis that yields a deterministic bound on the relative approximation error introduced by qdot. Empirical tests are performed to illustrate the tightness of the derived error bound and to demonstrate the effectiveness of qdot on a synthetic dataset, as well as two scientific benchmarks---the conjugate gradient (CG) and power methods. In some instances, using qdot for the dot products in CG can result in many components being quantized to half precision without increasing the iteration count required for convergence to the same solution as CG using a double precision dot product.