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At least 613 records · Page 34

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DOE OSTI2021

The IDAES process modeling framework and model library—Flexibility for process simulation and optimization

Abstract Energy systems and manufacturing processes of the 21st century are becoming increasingly dynamic and interconnected, which require new capabilities to effectively model and optimize their design and operations. Such next generation computational tools must leverage state‐of‐the‐art techniques in optimization and be able to rapidly incorporate new advances. To address these requirements, we have developed the Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform, which builds on the strengths of both process simulators (model libraries) and algebraic modeling languages (advanced solvers). This paper specifically presents the IDAES Core Modeling Framework (IDAES‐CMF), along with a case study demonstrating the application of the framework to solve process optimization problems. Capabilities provided by this framework include a flexible, modifiable, open‐source platform for optimization of process flowsheets utilizing state‐of‐the‐art solvers and solution techniques, fully open and extensible libraries of dynamic unit operations models and thermophysical property models, and integrated support for superstructure‐based conceptual design and optimization under uncertainty.

42 ENGINEERING↗

DOE OSTI2016

Pressure-Induced Bandgap Optimization in Lead-Based Perovskites with Prolonged Carrier Lifetime and Ambient Retainability

Bond length and bond angle exhibited by valence electrons is essential to the core of chemistry. Using lead-based organic–inorganic perovskite compounds as an exploratory platform, it is demonstrated that the modulation of valence electrons by compression can lead to discovery of new properties of known compounds. Yet, despite its unprecedented progress, further efficiency boost of lead-based organic–inorganic perovskite solar cells is hampered by their wider bandgap than the optimum value according to the Shockley–Queisser limit. By modulating the valence electron wavefunction with modest hydraulic pressure up to 2.1 GPa, the optimized bandgap for single-junction solar cells in lead-based perovskites, for the first time, is achieved by narrowing the bandgap of formamidinium lead triiodide (HC(NH 2 ) 2 PbI 3 ) from 1.489 to 1.337 eV. Strikingly, such bandgap narrowing is partially retained after the release of pressure to ambient, and the bandgap narrowing is also accompanied with double-prolonged carrier lifetime. With First-principles simulation, this work opens a new dimension in basic chemical understanding of structural photonics and electronics and paves an alternative pathway toward better photovoltaic materials-by-design.

14 SOLAR ENERGY↗

DOE OSTI2024

MITgcm-AD v2: Open source tangent linear and adjoint modeling framework for the oceans and atmosphere enabled by the Automatic Differentiation tool Tapenade

The Massachusetts Institute of Technology General Circulation Model (MITgcm) is widely used by the climate science community to simulate planetary atmosphere and ocean circulations. A defining feature of the MITgcm is that it has been developed to be compatible with an algorithmic differentiation (AD) tool, TAF, enabling the generation of tangent-linear and adjoint models. These provide gradient information which enables dynamics-based sensitivity and attribution studies, state and parameter estimation, and rigorous uncertainty quantification. Importantly, gradient information is essential for computing comprehensive sensitivities and performing efficient large-scale data assimilation, ensuring that observations collected from satellites and in-situ measuring instruments can be effectively used to optimize a large uncertain control space. As a result, the MITgcm forms the dynamical core of a key data assimilation product employed by the physical oceanography research community: Estimating the Circulation and Climate of the Ocean (ECCO) state estimate. Although MITgcm and ECCO are used extensively within the research community, the AD tool TAF is proprietary and hence inaccessible to a large proportion of these users. The new version 2 (MITgcm-AD v2) framework introduced here is based on the source-to-source AD tool Tapenade, which has recently been open-sourced. Another feature of Tapenade is that it stores required variables by default (instead of recomputing them) which simplifies the implementation of efficient, AD-compatible code. The framework has been integrated with the MITgcm model’s main branch and is now freely available.

Adjoints↗

DOE OSTI2020

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Direct comparison of gyrokinetic and fluid scrape-off layer simulations

Typically, fluid simulations are used for tokamak divertor design. However, fluid models are only valid if the scrape-off layer (SOL) is highly collisional. This assumption is valid in many present-day experiments but is questionable in the upstream SOL of some high-power scenarios envisioned for burning plasmas and fusion pilot plants. This paper reports on comparisons between fluid and kinetic simulations of the SOL for upstream parameters and geometry representative of the Spherical Tokamak for Energy Production fusion pilot plant. The SOLPS-ITER (fluid) and Gkeyll (gyrokinetic) codes are operated in a two-dimensional axisymmetric mode, which replaces turbulence with ad-hoc diffusivities. In kinetic simulations, we observe that the ions in the upstream SOL experience significant mirror trapping. This substantially increases the upstream temperature and has important implications for impurity dynamics. We show that the mirror force, which is excluded in SOLPS’s fluid equations, enhances the electrostatic potential drop along the field line in the SOL. We also show that the assumption of equal main ion and impurity temperatures, which is made in commonly used fluid codes, is invalid for the regimes explored here. The combination of these effects results in superior confinement of impurities to the divertor region in kinetic simulations, consistent with our earlier predictions [Kotschenreuther et al., in 29th IAEA 29 Fusion Energy Conference (IAEA, London, UK, 2023)]. This effect can be dramatic, reducing the midplane impurity density by orders of magnitude. These results indicate that in lower collisionality SOL’s the tolerable downstream impurity densities may be higher than would be predicted by fluid simulations, allowing for higher radiated power while avoiding unacceptable core contamination. Our results highlight the importance of kinetic simulations for divertor design and optimization for fusion pilot plants.

Computational fluid dynamics↗

DOE OSTI2024

MONKES: a fast neoclassical code for the evaluation of monoenergetic transport coefficients in stellarator plasmas

Abstract MONKES is a new neoclassical code for the evaluation of monoenergetic transport coefficients in stellarators. By means of a convergence study and benchmarks with other codes, it is shown that MONKES is accurate and efficient. The combination of spectral discretization in spatial and velocity coordinates with block sparsity allows MONKES to compute monoenergetic coefficients at low collisionality, in a single core, in approximately one minute. MONKES is sufficiently fast to be integrated into stellarator optimization codes for direct optimization of the bootstrap current and to be included in predictive transport suites. The code and data from this paper are available at https://github.com/JavierEscoto/MONKES/ .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Modeling Data Movement Performance on Heterogeneous Architectures

The cost of data movement on parallel systems varies greatly with machine architecture, job partition, and nearby jobs. Performance models that accurately capture the cost of data movement provide a tool for analysis, allowing for communication bottlenecks to be pinpointed. Modern heterogeneous architectures yield increased variance in data movement as there are a number of viable paths for inter-GPU communication. In this paper, we present performance models for the various paths of inter-node communication on modern heterogeneous architectures, including the trade-off between GPUDirect communication and copying to CPUs. Furthermore, we present a novel optimization for inter-node communication based on these models, utilizing all available CPU cores per node. Finally, we show associated performance improvements for MPI collective operations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

An Evaluation of One-Sided and Two-Sided Communication Paradigms on Relaxed-Ordering Interconnect

The Cray Gemini interconnect hardware provides multiple transfer mechanisms and out-of-order message delivery to improve communication throughput. In this paper we quantify the performance of one-sided and two-sided communication paradigms with respect to: 1) the optimal available hardware transfer mechanism, 2) message ordering constraints, 3) per node and per core message concurrency. In addition to using Cray native communication APIs, we use UPC and MPI micro-benchmarks to capture one- and two-sided semantics respectively. Our results indicate that relaxing the message delivery order can improve performance up to 4.6x when compared with strict ordering. When hardware allows it, high-level one-sided programming models can already take advantage of message reordering. Enforcing the ordering semantics of two-sided communication comes with a performance penalty. Furthermore, we argue that exposing out-of-order delivery at the application level is required for the next-generation programming models. Any ordering constraints in the language specifications reduce communication performance for small messages and increase the number of active cores required for peak throughput.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Scaling Semantic Graph Databases in Size and Performance

In this paper we present SGEM, a full software system for accelerating large-scale semantic graph databases on commodity clusters. Unlike current approaches, SGEM addresses semantic graph databases by only employing graph methods at all the levels of the stack. On one hand, this allows exploiting the space efficiency of graph data structures and the inherent parallelism of graph algorithms. These features adapt well to the increasing system memory and core counts of modern commodity clusters. On the other hand, however, these systems are optimized for regular computation and batched data transfers, while graph methods usually are irregular and generate fine-grained data accesses with poor spatial and temporal locality. Our framework comprises a SPARQL to data parallel C compiler, a library of parallel graph methods and a custom, multithreaded runtime system. We introduce our stack, motivate its advantages with respect to other solutions and show how we solved the challenges posed by irregular behaviors. We present the result of our software stack on the Berlin SPARQL benchmarks with datasets up to 10 billion triples (a triple corresponds to a graph edge), demonstrating scaling in dataset size and in performance as more nodes are added to the cluster.

Aggregation↗

DOE OSTI2016

SU-F-T-505: A Novel Approach for Sparing Critical Organs at Risk for Cancer Patients Undergoing Radiation Oncology Treatments

Purpose: A major goal of an effective radiation treatment plan is to deliver the maximum dose to the tumor while minimizing radiation exposure to the surrounding normal structures. For example, due to the radiation exposure to neighboring critical structures during prostate cancer treatment, a significant increase in cancer risk was observed for the bladder (77%) and the rectum (105%) over the following decade. Consequently, an effective treatment plan necessitates limiting the exposure to such organs which can best be achieved by physically displacing the organ at-risk. The goal of this study is to present a prototype for an organ re-positioner device designed and fabricated to physically move the rectum away from the path of radiation beam during external beam and brachytherapy treatments. This device affords patient comfort and provides a fully controlled motion to safely relocate the rectum during treatment. Methods: The NiTi shape memory alloy was designed and optimized for manufacturing a rectal re-positioner device through cooling and heating the core alloy for its shaping. This has been achieved through a prototyped custom designed electronic circuit in order to induce the reversible austenitic transformation and was tested rigorously to ensure the integrity of the actuated motion in displacement of the target anatomy. Results: The desirable NiTi shape-setting was configured for easy insertion and based on anatomical constraint. When the final prototype was evaluated, accuracy and precision of the maximum displacement and temperature changes revealed that the device could safely be used within the target anatomy. Conclusion: The organ re-positioner device is a promising tool that can be implemented in clinical setting. It provides a controlled and safe displacement of the delicate organ(s) at risk. The location of the organ being treated could also be identified using conventional onboard imaging devices or MV imaging available on-board most modern clinical accelerators.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Fast Mesh-to-Mesh Remaps Using Hash Algorithms

Here, we explore the potential uses of hash-based algorithms in the remap operation, mapping one computational mesh onto another. We implement and test optimizations designed to reduce memory operations and compare these optimizations in order to evaluate the performance impact across different meshes. In particular, we created a new remap method that creates a structured hierarchy of hashes. Tests were run on 2D meshes on up to 14 levels of mesh refinement and hundreds of millions of cells to measure the algorithms' relative speeds under differing circumstances. We show that our methods perform two orders of magnitude better than the standard kD-tree algorithm and that on different meshes different hash methods can be optimal. We explore these algorithms on serial CPUs, GPUs using OpenCL, and multi-core CPUs using OpenMP.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

PyBioNetFit

Systems biology models written in the BioNetGen language often contain parameters that must be fit based on experimental data. PyBioNetFit is a software tool designed to fit parameters of BioNetGen models. The user is expected to provide a BioNetGen model that contains unknown parameters, along with one or more text files containing experimental data. PyBioNetFit will perform a series of calls to the BioNetGen simulator using different parameter sets, to identify the parameter set that best fits the data. The parameter search is dictated by the user's choice of one of several metaheuristic optimization algorithms, including differential evolution, particle swarm optimization, scatter search, and simulated annealing. The software supports parallelized computing on multi-core computers and on computing clusters. We expect this software to be a useful tool for researchers designing BioNetGen models in collaboration with experimentalists.

Mitra, Eshan↗

DOE OSTI2018

Performance tuning of CEED software and first wave apps

The goal of this milestone was the performance tuning of the CEED software and first wave apps. In this milestone, the CEED team developed optimization techniques and tuned for performance the CEED software. Specifically, the focus was on the following: (1) Fast finite element operator storage and evaluation using partial assembly/matrix-free algorithms that take advantage of tensor-product element structure; (2) Architecture optimizations, including the development of performant discretization libraries targeting heterogeneous systems with multi-core CPUs, GPUs, and/or many-core CPUs in single node, cluster, or large-scale ECP supercomputer configurations; and (3) Global kernels for finite element operators, including the development of algorithms and libraries for fast gather-scatter exchanges for action assembly on unstructured graphs and for components needed for global linear solvers. A main part of this milestone was the performance tuning of the CEED first-wave ECP applications. This included the ExaSMR application – Coupled Monte Carlo Neutronics and Fluid Flow Simulation of Small Modular Reactors (ORNL), and the MARBL application – Next-Gen Multi-physics Simulation Code (LLNL). The artifacts delivered include performance improvements in CEED’s 1st wave of applications, and tuned CEED software for various architectures through a number of backends, freely available in the CEED’s repository on GitHub. See the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed for more details. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q4 of FY18 including: CEED’s second annual meeting, a successful minisymposium at the premier international conference on high-order methods (ICOSAHOM), making the CEED milestone reports publicly available, new Laghos release, and other outreach efforts.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Thermodynamic and Kinetic Modeling of Co-utilization of Glucose and Xylose for 2,3-BDO Production by Zymomonas mobilis

Prior engineering of the ethanologen Zymomonas mobilis has enabled it to metabolize xylose and to produce 2,3-butanediol (2,3-BDO) as a dominant fermentation product. When co-fermenting with xylose, glucose is preferentially utilized, even though xylose metabolism generates ATP more efficiently during 2,3-BDO production on a BDO-mol basis. To gain a deeper understanding of Z. mobilis metabolism, we first estimated the kinetic parameters of the glucose facilitator protein of Z. mobilis by fitting a kinetic uptake model, which shows that the maximum transport capacity of glucose is seven times higher than that of xylose, and glucose is six times more affinitive to the transporter than xylose. With these estimated kinetic parameters, we further compared the thermodynamic driving force and enzyme protein cost of glucose and xylose metabolism. It is found that, although 20% more ATP can be yielded stoichiometrically during xylose utilization, glucose metabolism is thermodynamically more favorable with 6% greater cumulative Gibbs free energy change, more economical with 37% less enzyme cost required at the initial stage and sustains the advantage of the thermodynamic driving force and protein cost through the fermentation process until glucose is exhausted. Glucose-6-phosphate dehydrogenase (g6pdh), glyceraldehyde-3-phosphate dehydrogenase (gapdh) and phosphoglycerate mutase (pgm) are identified as thermodynamic bottlenecks in glucose utilization pathway, as well as two more enzymes of xylose isomerase and ribulose-5-phosphate epimerase in xylose metabolism. Acetolactate synthase is found as potential engineering target for optimized protein cost supporting unit metabolic flux. Pathway analysis was then extended to the core stoichiometric matrix of Z. mobilis metabolism. Growth was simulated by dynamic flux balance analysis and the model was validated showing good agreement with experimental data. Dynamic FBA simulations suggest that a high agitation is preferable to increase 2,3-BDO productivity while a moderate agitation will benefit the 2,3-BDO titer. Taken together, this work provides thermodynamic and kinetic insights of Z. mobilis metabolism on dual substrates, and guidance of bioengineering efforts to increase hydrocarbon fuel production.

23-butanediol↗

DOE OSTI2018

Performance-Portable Particle Advection with VTK-m

Particle advection is the fundamental kernel behind most vector field visualization methods. Yet, the efficient parallel computation of large amounts of particle traces remains challenging. This is exacerbated by the variety of hardware trends in today's HPC arena, including increasing core counts in classical CPUs, many-core designs such as the Intel Xeon Phi, and massively parallel GPUs. The dedicated optimization of a particle advection kernel for each individual target architecture is both time-consuming and error prone. In this paper, we propose a performance-portable algorithm for particle advection. Our algorithm is based on the recently introduced VTK-m system and chiefly relies on its device adapter abstraction. We demonstrate the general portability of our implementation across a wide variety of hardware. Finally, our evaluation shows that our hardware-agnostic algorithm has comparable performance to hardware-specific algorithms.

Pugmire, Dave↗

DOE OSTI2023

Neutrino signatures of 100 2D Axisymmetric Core-Collapse Supernova Simulations

ABSTRACT We present in this paper a public data release of an unprecedentedly large set of core-collapse supernova (CCSN) neutrino emission models, comprising 100 detailed 2D axisymmetric radiation-hydrodynamic simulations evolved out to as late as ∼5 s post-bounce and spanning an extensive range of massive-star progenitors. The motivation for this paper is to provide a physically and numerically uniform benchmark data set to the broader neutrino detection community to help it characterize and optimize subsurface facilities for what is likely to be a once-in-a-lifetime galactic supernova burst event. With this release, we hope to (1) help the international experiment and modelling communities more efficiently optimize the retrieval of physical information about the next galactic CCSN, (2) facilitate the better understanding of core-collapse theory and modelling among interested experimentalists, and (3) help further integrate the broader supernova neutrino community.

Astronomy & Astrophysics↗

DOE OSTI2024

Dopant Segregation in Single-Crystal Optical Fiber Grown via the Laser-Heated Pedestal Growth Technique

Single crystal (SC) optical fiber has promising potential to be used for optical fiber sensing applications in harsh conditions due to its robustness to high temperature, high radioactivity, and resistance to chemical corrosion as compared to optical sensors using silica fiber. However, SC fiber grown via the laser-heated pedestal growth (LHPG) technique innately does not have a core-cladding structure found in standard optical fiber, resulting in optical losses. In this work we investigate optimization of the growth parameters of a two LHPG process used to grow SC fiber with a graded index via introduction of dopants to the feedstock material. Feedstock material is fabricated with the first LHPG device, then sol-gel dip-coated to create outer films of dopant material. The dip-coated feedstock is used to grow SC fiber in which segregation of the dopant constituents occurs, resulting in a graded index of refraction across the fiber, and an effective core-cladding structure. Hardware and software improvements to both LHPG systems are presented and the growth parameters for short pieces of ~320-330 μm diameter YAG fiber has been established. Characterization techniques/procedures have also been established for future grown SC fiber. These improvements and preparations are anticipated to result in a significant increase in grown fiber quality with a similar growth rate to that previously established.

Lander, Gary↗

DOE OSTI2024

Dopant Segregation in Single-Crystal Optical Fiber Grown via the Laser-Heated Pedestal Growth Technique

Lander, Gary↗