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DOE OSTI2017

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Graph-Based Representations and Applications to Process Simulation

Rapid and robust convergence of a process flowsheet is critical to enable large-scale simulations that address core scientific questions related to process design, optimization, and sustainability. However, due to the highly coupled and nonlinear nature of chemical processes, efficiently solving a flowsheet remains a challenge. In this work, we show that graph representations of the underlying physical phenomena in unit operations may help identify potential avenues to systematically reformulate the network of equations and enable more robust topology-based convergence of flowsheets. To this end, we developed graph abstractions of the governing equations of vapor-liquid and liquid-liquid equilibrium separation equipment. These graph abstractions consist of a mesh of interconnected variable nodes and equation nodes that are systematically generated through PhenomeNode, a new open-source library in Python developed in this study. We show that partitioning the graph into separate mass, energy, and equilibrium subgraphs can help decouple nonlinearities and guide decomposition algorithms. By employing the graph abstraction on an industrial separation process for separating glacial acetic acid from water, we implemented a new block decomposition scheme in BioSTEAM and demonstrated that this can accelerate convergence over a traditional sequential modular approach.

Distillation↗

DOE OSTI2019

Stochastic multiscale flux basis for Stokes-Darcy flows

Three algorithms are developed for uncertainty quantification in modeling coupled Stokes and Darcy flows. The porous media may consist of multiple regions with different properties. The permeability is modeled as a non-stationary stochastic variable, with its log represented as a sum of local Karhunen-Loève (KL) expansions. The problem is approximated by stochastic collocation on either tensor-product or sparse grids, coupled with a multiscale mortar mixed finite element method for the spatial discretization. A non-overlapping domain decomposition algorithm reduces the global problem to a coarse scale mortar interface problem, which is solved by an iterative solver, for each stochastic realization. In the traditional domain decomposition implementation, each subdomain solves a local Dirichlet or Neumann problem in every interface iteration. To reduce this cost, two additional algorithms based on deterministic or stochastic multiscale flux basis are introduced. The basis consists of the local flux (or velocity trace) responses from each mortar degree of freedom. It is computed for each subdomain independently before the interface iteration begins. The use of the multiscale flux basis avoids the need for subdomain solves on each iteration. The deterministic basis is computed at each stochastic collocation and used only at this realization. The stochastic basis is formed by further looping over all local realizations of a subdomain's KL region before the stochastic collocation begins. It is used over multiple realizations. Numerical tests are presented to illustrate the performance of the three algorithms, with the stochastic multiscale flux basis showing significant savings in computational cost compared to the other two algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

A Multiple-Set Overlapping-Domain Decomposed Monte Carlo Synthetic Acceleration Method for Linear Systems

We present a multiple-set overlapping-domain decomposed strategy for parallelizing the Monte Carlo Synthetic Acceleration method. Monte Carlo Synthetic Acceleration methods use the Neumann-Ulam class of Monte Carlo solvers for linear systems to accelerate a fixed-point iteration sequence. Effective parallel algorithms for these methods require the parallelization of the underlying Neumann-Ulam solvers. To do this in a domain decomposed environment, we borrow strategies traditionally implemented in Monte Carlo particle transport to parallelize the problem. The parallel Neumann-Ulam and multiple-set overlapping-domain decomposition algorithms are presented along with parallel scaling data for the resulting implementation using the Titan Cray XK7 machine at Oak Ridge National Laboratory.

Computer Science↗

DOE OSTI2022

On the Convergence of Overlapping Schwarz Decomposition for Nonlinear Optimal Control

Here, we study the convergence properties of an overlapping Schwarz decomposition algorithm for solving nonlinear optimal control problems (OCPs). The algorithm decomposes the time domain into a set of overlapping subdomains, and solves all subproblems defined over subdomains in parallel. The convergence is attained by updating primal-dual information at the boundaries of overlapping subdomains. We show that the algorithm exhibits local linear convergence, and that the convergence rate improves exponentially with the overlap size. We also establish global convergence results for a general quadratic programming, which enables the application of the Schwarz scheme inside second-order optimization algorithms (e.g., sequential quadratic programming). The theoretical foundation of our convergence analysis is a sensitivity result of nonlinear OCPs, which we call "exponential decay of sensitivity" (EDS). Intuitively, EDS states that the impact of perturbations at domain boundaries (i.e., initial and terminal time) on the solution decays exponentially as one moves into the domain. Here, we expand a previous analysis available in the literature by showing that EDS holds for both primal and dual solutions of nonlinear OCPs, under uniform second-order sufficient condition, controllability condition, and boundedness condition. We conduct experiments with a quadrotor motion planning problem and a partial differential equations (PDE) control problem to validate our theory, and show that the approach is significantly more efficient than alternating direction method of multipliers and as efficient as the centralized interior-point solver.

42 ENGINEERING↗

DOE OSTI2018

A Fast Solver for Implicit Integration of the Vlasov--Poisson System in the Eulerian Framework

In this paper, we present a domain decomposition algorithm to accelerate the solution of Eulerian-type discretizations of the linear, steady-state Vlasov equation. The steady-state solver then forms a key component in the implementation of fully implicit or nearly fully implicit temporal integrators for the nonlinear Vlasov--Poisson system. The solver relies on a particular decomposition of phase space that enables the use of sweeping techniques commonly used in radiation transport applications. The original linear system for the phase space unknowns is then replaced by a smaller linear system involving only unknowns on the boundary between subdomains, which can then be solved efficiently with Krylov methods such as GMRES. Steady-state solves are combined to form an implicit Runge--Kutta time integrator, and the Vlasov equation is coupled self-consistently to the Poisson equation via a linearized procedure or a nonlinear fixed-point method for the electric field. Finally, numerical results for standard test problems demonstrate the efficiency of the domain decomposition approach when compared to the direct application of an iterative solver to the original linear system.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

An efficient computational approach to model statistical correlations in photon counting x-ray detectors

Purpose: To introduce and evaluate an increment matrix approach (IMA) describing the signal statistics of energy-selective photon counting detectors including spatial–spectral correlations between energy bins of neighboring detector pixels. The importance of the occurring correlations for image-based material decomposition is studied. Methods: An IMA describing the counter increase patterns in a photon counting detector is proposed. This IMA has the potential to decrease the number of required random numbers compared to Monte Carlo simulations by pursuing an approach based on convolutions. To validate and demonstrate the IMA, an approximate semirealistic detector model is provided, simulating a photon counting detector in a simplified manner, e.g., by neglecting count rate-dependent effects. In this way, the spatial–spectral correlations on the detector level are obtained and fed into the IMA. The importance of these correlations in reconstructed energy bin images and the corresponding detector performance in image-based material decomposition is evaluated using a statistically optimal decomposition algorithm. Results: The results of IMA together with the semirealistic detector model were compared to other models and measurements using the spectral response and the energy bin sensitivity, finding a good agreement. Correlations between the different reconstructed energy bin images could be observed, and turned out to be of weak nature. These correlations were found to be not relevant in image-based material decomposition. An even simpler simulation procedure based on the energy bin sensitivity was tested instead and yielded similar results for the image-based material decomposition task, as long as the fact that one incident photon can increase multiple counters across neighboring detector pixels is taken into account. Conclusions: The IMA is computationally efficient as it required about 10{sup 2} random numbers per ray incident on a detector pixel instead of an estimated 10{sup 8} random numbers per ray as Monte Carlo approaches would need. The spatial–spectral correlations as described by IMA are not important for the studied image-based material decomposition task. Respecting the absolute photon counts and thus the multiple counter increases by a single x-ray photon, the same material decomposition performance could be obtained with a simpler detector description using the energy bin sensitivity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Data-Driven Adaptive Damping Controller for Wind Power Plants with Doubly-Fed Induction Generators

This paper presents an adaptive damping controller for wind power plants in which the turbines are equipped with doubly-fed induction generators. The controller is designed to respond to an input control signal that is triggered according to the system operating conditions. A processing unit continuously estimates the electromechanical modes of oscillation based on real-time streaming data acquired from a phasor measurement unit that is strategically positioned on the grid. The decision to trigger (or not trigger) the control signal is automatic, based on the relative damping of the dominant mode. The modes are estimated using the dynamic mode decomposition algorithm with time-delay embedding. Numerical simulations performed on the two-area system demonstrate that the proposed controller enhances the rotor angle stability for both small-signal and large disturbances, and is adaptive to changing grid conditions.

damping controller↗

DOE OSTI2020

Joint Planning of EV Fast Charging Stations and Power Distribution Systems With Balanced Traffic Flow Assignment

To tackle the challenges introduced by the fast-growing charging demand of electric vehicles (EVs), the power distribution systems (PDSs) and fast charging stations (FCSs) of EVs should be planned and operated in a more coordinated fashion. However, existing planning approaches generally aim to minimize investment costs in PDSs while ignoring the risk of worsening traffic conditions. To overcome this research gap, this article integrates the interests of traffic networks into PDS and FCS joint planning model to mitigate negative impacts on traffic conditions caused by installing FCSs. First, a novel microscopic method that is different from traditional assignment methods is proposed to simulate the influences of FCSs on traffic flows and EV charging loads. Then, a multiobjective joint planning model is developed to minimize both the planning costs and unbalanced traffic flows. A new bilayer Benders decomposition algorithm is designed to solve the proposed joint planning model. Numerical results on two practical systems in China validate the feasibility of our microscopic method by comparing the simulated results with real data. Compared with existing approaches, it is also demonstrated that the proposed joint planning approach helps to balance traffic flow assignments and relieve traffic congestion.

bilayer expanded Benders decomposition↗

DOE OSTI2021

Data-Driven Adaptive Damping Controller for Wind Power Plants with Doubly-Fed Induction Generators: Preprint

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2018

An Algorithm for Enhancing the Image Contrast of Electron Tomography

Abstract Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an individual particle of protein from a series of tilted angles. Individual-particle electron tomography (IPET) provides an approach for reconstructing a 3D density map from a single targeted protein particle (without averaging from different particles of this type of protein), in which the target particle was imaged from a series of tilting angles. However, owing to radiation damage limitations, low-dose images (high noise, and low image contrast) are often challenging to be aligned for 3D reconstruction at intermediate resolution (1–3 nm). Here, we propose a computational method to enhance the image contrast, without increasing any experimental dose, for IPET 3D reconstruction. Using an edge-preserving smoothing-based multi-scale image decomposition algorithm, this method can detect the object against a high-noise background and enhance the object image contrast without increasing the noise level or significantly decreasing the image resolution. The method was validated by using both negative staining (NS) ET and cryo-ET images. The successful 3D reconstruction of a small molecule (<100 kDa) indicated that this method can be used as a supporting tool to current ET 3D reconstruction methods for studying protein dynamics via structure determination from each individual particle of the same type of protein.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Resilient NdFeB magnet recycling under the impacts of COVID-19 pandemic: Stochastic programming and Benders decomposition

Neodymium-iron-boron (NdFeB) magnets are the most powerful magnets per unit volume sold in the commercial market. Despite the increasing demand for clean energy applications such as electric vehicles and wind turbines, disruptive events including the COVID-19 pandemic have caused significant uncertainties in the supply and demand for NdFeB magnets. Therefore, this study aims to alleviate the risk of supply shortage for NdFeB magnets and the containing critical materials, rare-earth elements (REEs), through the development of a resilient reverse supply chain and logistics network design. We develop scenarios to model the unique impact of the COVID-19 pandemic on the proposed business, incorporating both disruption intensity and recovery rate. We formulate a chance-constrained two-stage stochastic programming model to maximize the profit while guaranteeing the network resiliency against disruption risks. To solve the problem in large-scale instances, we develop an efficient Benders decomposition algorithm that reduces the computational time by 98.5% on average compared to the default CPLEX algorithm. When applied to the United States, the model suggests the optimal facility locations, processing capacities, inventory levels, and material flows for NdFeB magnet recyclers that could meet 99.7% of the demand. To the best of our knowledge, this study is the first to incorporate the impacts of the COVID-19 pandemic to design a resilient NdFeB magnet recycling supply chain and logistics network, leveraging risk-averse stochastic programming.

42 ENGINEERING↗

DOE OSTI2014

Phosphine-stabilised Au{sub 9} clusters interacting with titania and silica surfaces: The first evidence for the density of states signature of the support-immobilised cluster

Chemically made, atomically precise phosphine-stabilized clusters Au{sub 9}(PPh{sub 3}){sub 8}(NO{sub 3}){sub 3} were deposited on titania and silica from solutions at various concentrations and the samples heated under vacuum to remove the ligands. Metastable induced electron spectroscopy was used to determine the density of states at the surface, and X-ray photoelectron spectroscopy for analysing the composition of the surface. It was found for the Au{sub 9} cluster deposited on titania that the ligands react with the titania substrate. Based on analysis using the singular value decomposition algorithm, the series of MIE spectra can be described as a linear combination of 3 base spectra that are assigned to the spectra of the substrate, the phosphine ligands on the substrate, and the Au clusters anchored to titania after removal of the ligands. On silica, the Au clusters show significant agglomeration after heat treatment and no interaction of the ligands with the substrate can be identified.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Final Report, DE-FG01-06ER25718 Domain Decomposition and Parallel Computing

The goal of this project is to develop and improve domain decomposition algorithms for a variety of partial differential equations such as those of linear elasticity and electro-magnetics.These iterative methods are designed for massively parallel computing systems and allow the fast solution of the very large systems of algebraic equations that arise in large scale and complicated simulations. A special emphasis is placed on problems arising from Maxwell's equation. The approximate solvers, the preconditioners, are combined with the conjugate gradient method and must always include a solver of a coarse model in order to have a performance which is independent of the number of processors used in the computer simulation. A recent development allows for an adaptive construction of this coarse component of the preconditioner.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

A multistage distributionally robust optimization approach to water allocation under climate uncertainty

This paper investigates a Multistage Distributionally Robust Optimization (MDRO) approach to water allocation under climate uncertainty. The MDRO is formed by creating sets of conditional distributions (called conditional ambiguity sets) on a finite scenario tree. The distributions in the conditional ambiguity sets remain close to a nominal conditional distribution according a ø-divergence (e.g., Kullback-Leibler divergence, Hellinger distance, Burg entropy, etc.). Here, the paper discusses a decomposition algorithm to solve the resulting MDRO with ø-divergences, which uses the dual formulation and solves only linear subproblems instead of convex ones. Some properties of the algorithm such as generating feasible policies and valid upper/lower bounds are established. The paper then applies the modeling and solution techniques to allocate water in a rapidly-developing area of Tucson, Arizona. Tucson, like many arid and semi-arid regions around the world, faces considerable uncertainty in its ability to provide water for its citizens in the future. The primary sources of uncertainty in the Tucson region include (1) unpredictable population growth, (2) the availability of water from the Colorado River, and (3) the effects of climate variability on water consumption. This paper integrates forecasts for all these sources of uncertainty into a single optimization model for robust and sustainable water allocation. Then, it uses this model to analyze the value of constructing additional treatment facilities to reduce future water shortages. The results indicate that the MDRO approach can be very valuable for water managers by providing insights to minimize their risks and help them plan for the future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

WE-FG-207B-01: BEST IN PHYSICS (IMAGING): Abdominal CT with Three K-Edge Contrast Materials Using a Whole-Body Photon-Counting Scanner: Initial Results of a Large Animal Experiment

Purpose: To demonstrate the feasibility of in vivo three-material decomposition techniques using photon-counting CT (PCCT) with possible advantage of resolving arterial and venous flow of an organ simultaneously. Methods: Abdominal PCCT scans were acquired using a prototype whole-body PCCT with four energy thresholds (25/50/75/90keV) in a canine. Bismuth subsalicylate (60 mg) was administered orally one day prior to scanning. Immediately prior to CT scan, gadoteric acid (60 ml, Dotarem, Guerbet) was intravenously injected, followed in ten minutes by a 20mL injection of iodinated contrast (iopamidol 370 mg/mL, Bracco). Scans were acquired every ∼20 seconds, starting from the time of iodine injection. Linear material decomposition was performed using the least mean squares method to create concentration maps of iodine, gadolinium, and bismuth. The method was calibrated to vials with known concentrations of materials placed next to the animal. The accuracy of this method was tested on vials with known concentrations. Results: The material decomposition algorithm’s accuracy was confirmed to be within ±4mM in the test vials. In the animal, we could estimate the concentration of gadolinium in delayed-enhanced phase (10 minutes post-injection) in the abdomen. We could follow the wash-in and wash-out of iodine in arterial, venous, and excretory flow of the kidneys (20s, 80s, and 120s post-iodine injection) while gadolinium was present in the delayed-enhanced phase. Bismuth, which was used as a contrast agent for the gastro-intestinal tract, was easily differentiable from the other two contrast agents in the small intestine. Conclusion: This study shows the feasibility of using photon-counting CT with four energy thresholds to differentiate three k-edge contrast agents in vivo. This can potentially reduce radiation dose to patients by combining arterial and venous phases into a single acquisition.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

A New LMP-Sensitivity-Based Heterogeneous Decomposition for Transmission and Distribution Coordinated Economic Dispatch

Transmission and distribution coordinated economic dispatch (TDCED) will be necessary to settle the problems caused by high penetrations of distributed generators in future grids. An efficient heterogeneous decomposition algorithm (HGD) was proposed to solve the TDCED, but it may diverge occasionally. To overcome this shortcoming, a new HGD (N-HGD) with enhanced convergency is proposed and studied in this paper. Compared with the previous HGD, the N-HGD similarly decomposes the TDCED into transmission ED and distribution ED subproblems, but it considers the sensitivity of the boundary locational marginal price to load injections to enhance convergency and avoid divergence. Two kinds of sensitivity computing methods, M-c and M-p, are studied. M-c is based on a centralized sensitivity equation, executed on the transmission side. M-p is based on a probing mechanism and can be executed distributedly on the distribution side. The reason for the N-HGD's improved convergency is theoretically analyzed, and the optimality is proven. Numerical tests show that N-HGD performs better than the original HGD, as well as a penalty-based modified HGD that needs a careful parametertuning process. Furthermore, compared with M-c, an M-p-based N-HGD is preferable because it has a much lower computational cost and no additional communicational cost.

distribution↗

DOE OSTI2018

Stochastic Programming Approach for Resource Selection under Demand Uncertainty

Cost-efficient selection and scheduling of a subset of geographically distributed resources to meet the demands of a scientific workflow is a challenging problem. The problem is exacerbated by uncertainties in demand and availability of resources. In this paper, we present a stochastic optimization based framework for robust decision making in the selection of distributed resources over a planning horizon under demand uncertainty. We present a novel two-stage stochastic programming model for resource selection, and implement an L-shaped decomposition algorithm to solve this model. A Sample Average Approximation algorithm is integrated to enable stochastic optimization to solve problems with a large number of scenarios. Using the metric of stochastic solution, we demonstrate up to 30% cost reduction relative to solutions without explicit consideration of demand uncertainty for a 24-month problem. We also demonstrate up to 54% cost reduction relative to a previously developed solution for a 36-month problem. We further argue that the composition of resources selected is superior to solutions computed without explicit consideration of uncertainties. Given the importance of resource selection and scheduling of complex scientific workflows, especially in the context of commercial cloud computing, we believe that our novel stochastic programming framework will benefit many researchers as well as users of distributed computing resources.

scientific workflows, task scheduling, optimizatio↗