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At least 1,117 records · Page 62

Automatic mathematical modeling for real time simulation system

A methodology for automatic mathematical modeling and generating simulation models is described. The models will be verified by running in a test environment using standard profiles with the results compared against known results. The major objective is to create a user friendly environment for engineers to design, maintain, and verify their model and also automatically convert the mathematical model into conventional code for conventional computation. A demonstration program was designed for modeling the Space Shuttle Main Engine Simulation. It is written in LISP and MACSYMA and runs on a Symbolic 3670 Lisp Machine. The program provides a very friendly and well organized environment for engineers to build a knowledge base for base equations and general information. It contains an initial set of component process elements for the Space Shuttle Main Engine Simulation and a questionnaire that allows the engineer to answer a set of questions to specify a particular model. The system is then able to automatically generate the model and FORTRAN code. The future goal which is under construction is to download the FORTRAN code to VAX/VMS system for conventional computation. The SSME mathematical model will be verified in a test environment and the solution compared with the real data profile. The use of artificial intelligence techniques has shown that the process of the simulation modeling can be simplified.

Wang, Caroline↗

Learning nonlinear operators via DeepONet based on the universal approximation theorem of operators

It is widely known that neural networks (NNs) are universal approximators of continuous functions. However, a less known but powerful result is that a NN with a single hidden layer can accurately approximate any nonlinear continuous operator. This universal approximation theorem of operators is suggestive of the structure and potential of deep neural networks (DNNs) in learning continuous operators or complex systems from streams of scattered data. Here, in this work, we thus extend this theorem to DNNs. We design a new network with small generalization error, the deep operator network (DeepONet), which consists of a DNN for encoding the discrete input function space (branch net) and another DNN for encoding the domain of the output functions (trunk net). We demonstrate that DeepONet can learn various explicit operators, such as integrals and fractional Laplacians, as well as implicit operators that represent deterministic and stochastic differential equations. We study different formulations of the input function space and its effect on the generalization error for 16 different diverse applications.

97 MATHEMATICS AND COMPUTING↗

Next Generation Suspension Dynamics Algorithms

This research project has the objective to extend the range of application, improve the efficiency and conduct simulations with the Fast Lubrication Dynamics (FLD) algorithm for concentrated particle suspensions in a Newtonian fluid solvent. The research involves a combination of mathematical development, new computational algorithms, and application to processing flows of relevance in materials processing. The mathematical developments clarify the underlying theory, facilitate verification against classic monographs in the field and provide the framework for a novel parallel implementation optimized for an OpenMP shared memory environment. The project considered application to consolidation flows of major interest in high throughput materials processing and identified hitherto unforeseen challenges in the use of FLD in these applications. Extensions to the algorithm have been developed to improve its accuracy in these applications.

97 MATHEMATICS AND COMPUTING↗

Generalized trigonometric Fourier-series method with automatic time step control for non-linear point kinetics equations

The trigonometric Fourier-series method (TFS) is generalized to provide approximate solutions for non-linear point kinetics equations with feedback using varying step sizes. This method can provide a very stable solution against the size of the discrete time step allowing much larger step sizes to be used. Systems of the point kinetics equations are solved using Fourier-series expansion over a partition of the total time interval. The approximate solution requires determining the series coefficients over each time step in that partition. These coefficients are determined using the high-order derivatives of the solution vector at the beginning of the time step introducing a system of linear algebraic equations to be solved at each step. This system is similar to the Vandermonde system. Two successive orders of the partial sums are used to estimate the local truncation error. This error and some other constrains are used to produce the largest step size allowable at each step while keeping the error within a specific tolerance. The process of calculating suitable step sizes should be automatic and inexpensive. Convergence and stability of the proposed method are discussed and a new formula is introduced to maintain stability. The proposed method solves the general linear and non-linear kinetics problems. The method has been applied to five different types of reactivities including step/ramp insertions with temperature feedback. The method is seemed to be valid for larger time intervals than those used in the conventional numerical integration, and is thus useful in reducing computing time. Computational results are found to be consistent with the analysis, they demonstrate that the convergence of the iteration scheme can be accelerated and the resulting computing times can be greatly reduced while maintain computational accuracy.

97 MATHEMATICS AND COMPUTING↗

Synergistic Challenges in Data-Intensive Science and Exascale Computing. Summary report of the Advanced Scientific Computing Advisory Committee (ASCAC) Subcommittee, March 2013

The ASCAC Subcommittee on Synergistic Challenges in Data-Intensive Science and Exascale Computing has reviewed current practice and future plans in multiple science domains in the context of the challenges facing both Big Data and the Exascale Computing. challenges. The review drew from public presentations, workshop reports and expert testimony. Data-intensive research activities are increasing in all domains of science, and exascale computing is a key enabler of these activities. We briefly summarize below the key findings and recommendations from this report from the perspective of identifying investments that are most likely to positively impact both data-intensive science goals and exascale computing goals.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero User Manual (V.5.0)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero Theory Manual (V.5.0)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero Theory Manual (V.5.2)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero Theory Manual (V.5.4)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero User Manual (V.5.4)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero User Manual (V.5.10)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

Scalable metagenomic taxonomy classification using a reference genome database

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an offline computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take520 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample.

59 BASIC BIOLOGICAL SCIENCES↗

Kmer-SSR: a fast and exhaustive SSR search algorithm

Motivation: One of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a ‘good enough’ solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a ‘good enough’ solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions. Results: We present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm. Availability and implementation: The source code is freely available on GitHub at https://github. com/ridgelab/Kmer-SSR.

59 BASIC BIOLOGICAL SCIENCES↗

Robust Containment Queries over Collections of Rational Parametric Curves via Generalized Winding Numbers

Point containment queries for regions bound by watertight geometric surfaces, i.e., closed and without self-intersections, can be evaluated straightforwardly with a number of well-studied algorithms. When this assumption on domain geometry is not met, such methods are either unusable, or prone to misclassifications that can lead to cascading errors in downstream applications. More robust point classification schemes based on generalized winding numbers have been proposed, as they are indifferent to these imperfections. However, existing algorithms are limited to point clouds and collections of linear elements. We extend this methodology to encompass more general curved shapes with an algorithm that evaluates the winding number scalar field over unstructured collections of rational parametric curves. In particular, we evaluate the winding number for each curve independently, making the derived containment query robust to how the curves are arranged. We ensure geometric fidelity in our queries by treating each curve as equivalent to an adaptively constructed polyline that provably has the same generalized winding number at the point of interest. Our algorithm is numerically stable for points that are arbitrarily close to the model, and explicitly treats points that are coincident with curves. We demonstrate the improvements in computational performance granted by this method over conventional techniques as well as the robustness induced by its application.

97 MATHEMATICS AND COMPUTING↗

Multiphysics Simulations: Challenges and Opportunities

We consider multiphysics applications from algorithmic and architectural perspectives, where ‘‘algorithmic’’ includes both mathematical analysis and computational complexity, and ‘‘architectural’’ includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

Keyes, David↗

Multiphysics Simulations: Challenges and Opportunities

We consider multiphysics applications from algorithmic and architectural perspectives, where "algorithmic" includes both mathematical analysis and computational complexity, and "architectural" includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

99 GENERAL AND MISCELLANEOUS↗

Math modeling and computer mechanization for real time simulation of rotary-wing aircraft

Mathematical modeling and computer mechanization for real time simulation of rotary wing aircraft is discussed. Error analysis in the digital simulation of dynamic systems, such as rotary wing aircraft is described. The method for digital simulation of nonlinearities with discontinuities, such as exist in typical flight control systems and rotor blade hinges, is discussed.

Howe, R. M.↗

Approximating the linear response of physical chaos

Abstract Parametric derivatives of statistics are highly desired quantities in prediction, design optimization and uncertainty quantification. In the presence of chaos, the rigorous computation of these quantities is certainly possible, but mathematically complicated and computationally expensive. Based on Ruelle’s formalism, this paper shows that the sophisticated linear response algorithm can be dramatically simplified in higher-dimensional systems featuring statistical homogeneity in the physical space. We argue that the contribution of the SRB (Sinai–Ruelle–Bowen) measure gradient, which is an integral yet the most cumbersome part of the full algorithm, is negligible if the objective function is appropriately aligned with unstable manifolds. This abstract condition could potentially be satisfied by a vast family of real-world chaotic systems, regardless of the physical meaning and mathematical form of the objective function and perturbed parameter. We demonstrate several numerical examples that support these conclusions and that present the use and performance of a simplified linear response algorithm. In the numerical experiments, we consider physical models described by differential equations, including Lorenz 96 and Kuramoto–Sivashinsky.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗