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At least 865 records · Page 48

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical sciences by providing tools to support and guide the experimental effort and for prediction of chemical and materials properties. In this regard, a special role has been played by electronic structure packages where complex chemical and materials processes can be modeled using first-principle-driven methodologies. Over the last few decades, the rapid development of computing technologies and a tremendous increase in computational power has offered a unique chance to study complex chemical transformations using sophisticated and predictive many-body techniques to describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, a critical role has been played by novel parallel algorithms capable of taking advantage of computational resources to address polynomial scaling of electronic structure methods. NWChem was among the first electronic structure codes that focused on delivering scalable performance for electronic structure simulations. Herein, we briefly review the NWChem suite of computational codes including its history, design principles, parallel tools, current capabilities, outreach and outlook.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assignment Of Finite Elements To Parallel Processors

Elements assigned approximately optimally to subdomains. Mapping algorithm based on simulated-annealing concept used to minimize approximate time required to perform finite-element computation on hypercube computer or other network of parallel data processors. Mapping algorithm needed when shape of domain complicated or otherwise not obvious what allocation of elements to subdomains minimizes cost of computation.

Salama, Moktar A.↗

On the stability of nongyrotropic ion populations - A first (analytic and simulation) assessment

The wave and dispersion equations for perturbations propagating parallel to an ambient magnetic field in magnetoplasmas with nongyrotropic ion populations show, in general, the occurrence of coupling between the parallel (left- and right-hand circularly polarized electromagnetic and longitudinal electrostatic) eigenmodes of the associated gyrotropic medium. These interactions provide a means to driving linearly one mode with free-energy sources of other modes in homogeneous media. Different types of nongyrotropy bring about distinct classes of coupling. The stability of a hydrogen magnetoplasma with anisotropic, nongyrotropic protons that only couple the electromagnetic modes to each other is investigated analytically (via solution of the derived dispersion equation) and numerically (via simulation with a hybrid code). Nongyrotropy enhances growth and enlarges the unstable spectral range relative to the corresponding gyrotropic situation. The relevance of the properties of nongyrotropic populations to space plasma environments is also discussed.

Brinca, A. L.↗

Plasma heating at collisionless shocks due to the kinetic cross-field streaming instability

Heating at collisionless shocks due to the kinetic cross-field streaming instability, which is the finite beta (ratio of plasma to magnetic pressure) extension of the modified two stream instability, is studied. Heating rates are derived from quasi-linear theory and compared with results from particle simulations to show that electron heating relative to ion heating and heating parallel to the magnetic field relative to perpendicular heating for both the electrons and ions increase with beta. The simulations suggest that electron dynamics determine the saturation level of the instability, which is manifested by the formation of a flattop electron distribution parallel to the magnetic field. As a result, both the saturation levels of the fluctuations and the heating rates decrease sharply with beta. Applications of these results to plasma heating in simulations of shocks and the earth's bow shock are described.

Winske, D.↗

Simulation of an array-based neural net model

Research in cognitive science suggests that much of cognition involves the rapid manipulation of complex data structures. However, it is very unclear how this could be realized in neural networks or connectionist systems. A core question is: how could the interconnectivity of items in an abstract-level data structure be neurally encoded? The answer appeals mainly to positional relationships between activity patterns within neural arrays, rather than directly to neural connections in the traditional way. The new method was initially devised to account for abstract symbolic data structures, but it also supports cognitively useful spatial analogue, image-like representations. As the neural model is based on massive, uniform, parallel computations over 2D arrays, the massively parallel processor is a convenient tool for simulation work, although there are complications in using the machine to the fullest advantage. An MPP Pascal simulation program for a small pilot version of the model is running.

Barnden, John A.↗

Dayflow: CONUS Daily Streamflow Reanalysis, Version 1 (V1)

Dayflow V1 is a historical streamflow reanalysis dataset reconstructed for a 36-year period (1980-2015). The dataset provides both daily and monthly scale streamflow information at about 2.7 million NHDPlusV2 stream reaches in the conterminous US (CONUS). Dayflow is the result of a nationally scalable modeling framework that integrates the simulated runoff from the Variable Infiltration Capacity (VIC) model with the Routing Application for Parallel computatIon of Discharge (RAPID) routing model. Two types of streamflow products, simulated streamflow with or without assimilation of historic US Geological Survey (USGS) streamflow observations, are provided in Dayflow V1. A comprehensive evaluation at 7,526 USGS National Water Information System (NWIS) gauges is performed for both types of streamflow products. The resulting key evaluation metrics are also included in the Dayflow V1 Dataset.

13 HYDRO ENERGY↗

PySAGES: flexible, advanced sampling methods accelerated with GPUs

Abstract Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a broad range of complex systems is essential. Building on past efforts to provide open-source community-supported software for advanced sampling, we introduce PySAGES, a Python implementation of the Software Suite for Advanced General Ensemble Simulations (SSAGES) that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces, harmonic bias, or forward flux sampling in the context of molecular dynamics simulations. By providing an intuitive interface that facilitates the management of a system’s configuration, the inclusion of new collective variables, and the implementation of sophisticated free energy-based sampling methods, the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques. The capabilities, core features, and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems. We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations, improve sampling, and enable facile estimation of free energies for a wide range of materials and processes.

Chemistry↗

Effect of Anoxic Iron Corrosion on WIPP Brine Geochemistry FY23 Final Report (U)

A 280-day study was completed to evaluate the effect of zero-valent iron (Fe 0 ) on the Waste Isolation Pilot Plant (WIPP) brine geochemistry under anticipated reducing conditions. Hydrogen (H 2 ) gas is expected to be present in the repository after closure due to the anoxic corrosion of a vast quantity of iron contained in the waste forms disposed at WIPP; therefore, a background argon atmosphere containing H 2 was chosen for this study. WIPP groundwater brine pH and E h will impact the mobility and fate of plutonium within the repository. Modeling and laboratory results for Castile WIPP brine indicate that equilibrium fa values relative to the standard hydrogen electrode (SHE) are 40 mV more reducing (i.e., more negative) than those for Salado WIPP brine (-480 mV vs. -440 mV, respectively) because of the higher pH of the Castile brine (pH 9 .3 for Castile vs. pH 8.8 for Salado). The E h and pH data were corrected for the effects of high ionic strength. The experimental results for both brines are consistent with thermodynamic predictions using OLI Systems' Mixed Solvent Electrolyte chemical equilibrium model. The measured and corrected pH and E h data from this study are provided in Table ES-I and Table ES-2, respectively. The experimental study, with four test conditions in triplicate, was performed in a dual glovebox with a nominally 3 vol.% H 2 in argon atmosphere (target H 2 range: 3 ± I vol.%). Simulants containing MgO only ( experimental control) and MgO+Fe 0 (WIPP base case) were prepared for both the Salado and Castile brines. MgO was included in all simulants to account for the use of bulk magnesium oxide in the WIPP repository. Fe 0 was included in some simulants to incorporate the effects of the anoxic corrosion of iron and in-situ hydrogen generation in the study. The brine compositions were developed by Sandia National Laboratory (SNL; Xiong, 2008) and have been used in previous WIPP evaluations. The test method (agitation, etc.) is partially based on ASTM D3987-12. Twelve rounds of periodic measurements of pH and E h were performed over the course of the study. Chemical analysis results for liquids and solids (ICP-MS, ICP-ES, IC Anion, TIC, SEM-EDX) are consistent with the pH, E h , and thermodynamic modeling results. This study included the following conditions that deviate from anticipated post-closure conditions following brine intrusion, but were selected to facilitate bench-scale testing to validate modeling of pH and E h for the post-closure WIP P repository: an anoxic glove box atmosphere containing ≤ 4 vol. % H 2 vs. substantially higher H 2 gas concentrations assumed in the WIPP Performance Assessment (PA); a significantly higher liquid-to-solid test ratio compared to the much lower phase ratio anticipated in the WIP P repository; agitation of the simulant bottles to maximize mass transfer; and finally the use of Fe 0 reagents having a much greater surface area than expected in the WIP P repository. Non-representative conditions were chosen for various reasons such as: to provide bounding conservative results, to provide a margin of safety for testing, or to facilitate simulant sub-sampling and analysis. In a parallel effort, aqueous electrolyte thermodynamic models were developed for the synthetic Salado and Castile brines to inform the experimental design, facilitate laboratory data interpretation, and allow extension of evaluations beyond the parameters tested. Thermodynamic modeling simulations including the MgO and Fe 0 additives that are directly relevant to the experimental measurements (e.g., pH calibration curve, ORP corrections) are included in this report. The measured fa of the simulants was close to the OLI model predictions for both brines and was largely controlled by the background H 2 partial pressure in the vapor phase as well as H 2 generated in situ in the aqueous phase by the Fe 0 corrosion. The H 2 gas-phase concentration tested and thermodynamically evaluated was much lower than is assumed in the WIPP PA; however, H 2 (g) concentrations significantly below this level are still predicted to result in very reducing conditions. In conclusion: • The experimental results are consistent with thermodynamic model predictions for fa, pH, and the effects of high ionic strength. • Evidence to date suggests that the H2 concentration in the glovebox atmosphere ultimately determined the final E h values of the simulants and resulted in highly reducing conditions. As a result, little difference was observed between the control simulants containing only MgO and the WIPP base-case simulants that contained MgO and Fe 0 . • This test methodology is recommended for future studies evaluating WIPP repository conditions. The methodology includes: (1) background H 2 in argon with agitation ( or could alternatively include in-situ-generated H 2 in sealed bottles); (2) carefully measured and corrected ORP data ( with much effort focused on allowing the probes to fully stabilize); and (3) ionic-strength-corrected pH data. Other best practices, such as simulant sparging/handling, ORP probe replacement, etc., should also be considered. • The coupling of experimental studies and thermodynamic modeling is also highly recommended because these methods inform and direct one another leading to greater confidence in and understanding of the results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

CaTS: Integration of Geant4 and Opticks

CaTS [6]is an advanced example that is part of Geant4 since version 11.0. It demonstrates the use of Opticks to offload the simulation of optical photons to GPUs. Opticks interfaces with the Geant4 toolkit to collect all the necessary information to generate and trace optical photons, re-implements the optical physics processes to be run on the GPU, and automatically translates the Geant4 geometry into a GPU appropriate format. To trace the photons, Opticks uses NVIDIA OptiX®. In this report, we describe CaTS and the integration of Opticks with Geant4. We demonstrate that the generation and tracing of optical photons represents an ideal application to be offloaded to GPUs, fully utilizing the high degree of available parallelism. In a typical liquid argon TPC simulation, a speedup of several hundred times is observed compared to an equivalent simulation using single threaded Geant4.

Wenzel, Hans↗

Parallelization of Rocket Engine System Software (Press)

The main goal is to assess parallelization requirements for the Rocket Engine Numeric Simulator (RENS) project which, aside from gathering information on liquid-propelled rocket engines and setting forth requirements, involve a large FORTRAN based package at NASA Lewis Research Center and TDK software developed by SUBR/UWF. The ultimate aim is to develop, test, integrate, and suitably deploy a family of software packages on various aspects and facets of rocket engines using liquid-propellants. At present, all project efforts by the funding agency, NASA Lewis Research Center, and the HBCU participants are disseminated over the internet using world wide web home pages. Considering obviously expensive methods of actual field trails, the benefits of software simulators are potentially enormous. When realized, these benefits will be analogous to those provided by numerous CAD/CAM packages and flight-training simulators. According to the overall task assignments, Hampton University's role is to collect all available software, place them in a common format, assess and evaluate, define interfaces, and provide integration. Most importantly, the HU's mission is to see to it that the real-time performance is assured. This involves source code translations, porting, and distribution. The porting will be done in two phases: First, place all software on Cray XMP platform using FORTRAN. After testing and evaluation on the Cray X-MP, the code will be translated to C + + and ported to the parallel nCUBE platform. At present, we are evaluating another option of distributed processing over local area networks using Sun NFS, Ethernet, TCP/IP. Considering the heterogeneous nature of the present software (e.g., first started as an expert system using LISP machines) which now involve FORTRAN code, the effort is expected to be quite challenging.

Cezzar, Ruknet↗

Nonlinear Landau damping and Alfven wave dissipation

Nonlinear Landau damping has been often suggested to be the cause of the dissipation of Alfven waves in the solar wind as well as the mechanism for ion heating and selective preacceleration in solar flares. We discuss the viability of these processes in light of our theoretical and numerical results. We present one-dimensional hybrid plasma simulations of the nonlinear Landau damping of parallel Alfven waves. In this scenario, two Alfven waves nonresonantly combine to create second-order magnetic field pressure gradients, which then drive density fluctuations, which in turn drive a second-order longitudinal electric field. Under certain conditions, this electric field strongly interacts with the ambient ions via the Landau resonance which leads to a rapid dissipation of the Alfven wave energy. While there is a net flux of energy from the waves to the ions, one of the Alfven waves will grow if both have the same polarization. We compare damping and growth rates from plasma simulations with those predicted by Lee and Volk (1973), and also discuss the evolution of the ambient ion distribution. We then consider this nonlinear interaction in the presence of a spectrum of Alfven waves, and discuss the spectrum's influence on the growth or damping of a single wave. We also discuss the implications for wave dissipation and ion heating in the solar wind.

Vinas, Adolfo F.↗

Preliminary Observing System Simulation Experiments for Doppler Wind Lidars Deployed on the International Space Station

NASA Goddard Space Flight Center's Software Systems Support Office (SSSO) is participating in a multi-agency study of the impact of assimilating Doppler wind lidar observations on numerical weather prediction. Funded by NASA's Earth Science Technology Office, SSSO has worked with Simpson Weather Associates to produce time series of synthetic lidar observations mimicking the OAWL and WISSCR lidar instruments deployed on the International Space Station. In addition, SSSO has worked to assimilate a portion of these observations those drawn from the NASA fvGCM Nature Run into the NASA GEOS-DAS global weather prediction system in a series of Observing System Simulation Experiments (OSSEs). These OSSEs will complement parallel OSSEs prepared by the Joint Center for Satellite Data Assimilation and by NOAA's Atlantic Oceanographic and Meteorological Laboratory. In this talk, we will describe our procedure and provide available OSSE results.

Observing System Simulation↗

Simulations of active ion injection experiments on ARCS 3

The ARCS 3 sounding rocket experiment used two argon guns oriented parallel and perpendicular to the geomagnetic field. The parameters of this experiment have been used in a series of particle simulations in order to interpret ion beam interaction with the multispecies ionospheric plasma. Along with the lower hybrid mode between the electron and the hydrogen gyrofrequencies, ion-ion hybrid modes between the hydrogen and helium gyrofrequencies and between the helium and oxygen gyrofrequencies are identified in the simulations. Besides these cold plasma modes, warm Bernstein modes of the respective ion species are identified. The parallel argon beam injections excite lower hybrid waves perpendicular to the magnetic field because of the finite thermal spread of the parallel beam. Perpendicular ion heating of background hydrogen, helium, and oxygen is comparable in the simulations. Comparisons are made with the wave and particle data from the ARCS 3 rocket experiment.

Hudson, M. K.↗

Analysis of hypercube cache performance using address traces generated by TRAPEDS

The authors utilize a recently developed software method of capturing and analyzing address traces, known as TRAPEDS (TRAce Producing Execution Driven Simulation), to provide address traces for cache performance evaluation on a hypercube multicomputer. Utilizing TRAPEDS user code traces obtained from the implementations of several parallel algorithms on the Intel iPSC/2 hypercube, the authors simulate the cache performance effects of changing cache size, line size, and set associativity. Particular attention is devoted to the effect on cache performance of changing the dimension of the hypercube for a particular program and to the variation in cache statistics among the nodes of the hypercube.

Stunkel, Craig B.↗

Massively parallel transport sweeps on meshes with cyclic dependencies

When solving the first-order form of the linear Boltzmann equation, a common misconception is that the matrix-free computational method of “sweeping the mesh”, used in conjunction with the Discrete Ordinates method, is too complex or does not scale well enough to be implemented in modern high performance computing codes. This has led to considerable efforts in the development of matrix-based methods that are computationally expensive and is partly driven by the requirements placed on modern spatial discretizations. In particular, modern transport codes are required to support higher order elements, a concept that invariably adds a lot of complexity to sweeps because of the introduction of cyclic dependencies with curved mesh cells. In this article we will present a comprehensive implementation of sweeping, to a piecewise-linear DFEM spatial discretization with particular focus on handling cyclic dependencies and possible extensions to higher order spatial discretizations. We find that these methods are implemented in a new C++ simulation framework called Chi-Tech (). We present some typical simulation results with some performance aspects that one can expect during real world simulations, we also present a scaling study to >100k processes where Chi-Tech maintains greater than 80% efficiency solving a total of 87.7 trillion angular flux unknowns for a 116 group simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

MOOSE: A Modular Platform for Fission and Fusion Multiphysics

The Multiphysics Object-Oriented Simulation Environment (MOOSE) Framework, as well as MOOSE-based simulation tools, have accelerated the development of fission energy and advanced reactor technologies through the United States Department of Energy, Office of Nuclear Science, Nuclear Energy Advanced Modeling & Simulation (NEAMS) Program. MOOSE contains a complete platform of multiphysics simulation capabilities, capable of running on massively parallel systems, and is developed in an open-source manner with great attention paid to high-quality software quality assurance practices. This overall approach could greatly benefit the fusion energy community, which requires rapid design iteration and improvement in order to facilitate the successful development of fusion as an alternative energy source to fossil fuels. In the first half of this talk, applications of MOOSE and MOOSE-based tools for advanced reactor designs will be showcased, as well as MOOSE ecosystem infrastructure (such as the NEAMS Virtual Test Bed) that enables and accelerates fission reactor design. In the second half, a discussion of how the MOOSE approach to modeling and simulation is currently being applied internationally in fusion energy research and development at the United Kingdom Atomic Energy Authority will be discussed, and ongoing/future domestic research efforts will be highlighted.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Latent Twins

Over the past decade, scientific machine learning has transformed the development of mathematical and computational frameworks for analyzing, modeling, and predicting complex systems. From inverse problems to numerical partial differential equations (PDEs), dynamical systems, and model reduction, these advances have pushed the boundaries of what can be simulated. Yet they have often progressed in parallel, with representation learning and algorithmic solution methods evolving largely as separate pipelines. With Latent Twins, we propose a unifying mathematical framework that creates a hidden surrogate in latent space for the underlying equations. Whereas digital twins mirror physical systems in the digital world, Latent Twins mirror mathematical systems in a learned latent space governed by operators. Through this lens, classical modeling, inversion, model reduction, and operator approximation all emerge as special cases of a single principle. We establish the fundamental approximation properties of Latent Twins for both ordinary differential equations (ODEs) and PDEs and demonstrate the framework across three representative settings: (i) canonical ODEs, capturing diverse dynamical regimes; (ii) a PDE benchmark using the shallow-water equations, contrasting Latent Twin simulations with deep operator network and forecasts with a four-dimensional variational method baseline; and (iii) a challenging real-data geopotential reanalysis dataset, reconstructing and forecasting from sparse, noisy observations. Latent Twins provide a compact, interpretable surrogate for solution operators that evaluate across arbitrary time gaps in a single-shot, while remaining compatible with scientific pipelines such as assimilation, control, and uncertainty quantification. Looking forward, this framework offers scalable, theory-grounded surrogates that bridge data-driven representation learning and classical scientific modeling across disciplines.

Latent Twins↗

GeantV: Results from the Prototype of Concurrent Vector Particle Transport Simulation in HEP

Full detector simulation was among the largest CPU consumers in all CERN experiment software stacks for the first two runs of the Large Hadron Collider. In the early 2010s, it was projected that simulation demands would scale linearly with increasing luminosity, with only partial compensation from increasing computing resources. The extension of fast simulation approaches to cover more use cases that represent a larger fraction of the simulation budget is only part of the solution, because of intrinsic precision limitations. The remainder corresponds to speeding up the simulation software by several factors, which is not achievable by just applying simple optimizations to the current code base. In this context, the GeantV R&D project was launched, aiming to redesign the legacy particle transport code in order to benefit from features of fine-grained parallelism, including vectorization and increased locality of both instruction and data. This paper provides an extensive presentation of the results and achievements of this R&D project, as well as the conclusions and lessons learned from the beta version prototype.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗