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At least 1,153 records · Page 64

MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. In conclusion, MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

97 MATHEMATICS AND COMPUTING↗

A scalable framework for the global offline community land model ensemble simulation

Current earth system models have a large range of uncertainty, owing to differences in the simulation of feedbacks and insufficient information to constrain model parameters. Parameter disturbance experiment provides a straightforward method to quantify the variation (uncertainty) outputs caused by model inputs. Owing to the software complexity and computational intensity of earth system models, a large-scale simulation framework is needed to support ensemble simulation required by parameter disturbance experiment. This paper presents a parallel framework for the community land model ensemble simulation. After a software structure review of the community land model simulation, a single factor parameter disturbance experiment of a reference computational experiment design is used to demonstrate the software design principles, computational characteristics of individual application, parallel ensemble simulation implementation, as well as the weak scalability of this simulation framework on a high-end computer. Lastly, the paper discusses some preliminary diagnostic analysis results of the single factor parameter disturbance experiments. The framework design considerations and implementation details described in this paper can be beneficial to many other research programmes involving large scale, legacy modelling system.

58 GEOSCIENCES↗

The Effect of Aging on the Delamination Fracture Energy of Glass Solar Reflectors

Thin metal and metal oxide films deposited on glass or polymer substrates have been widely applied to manufacture front surfaced solar reflectors such as those used in the concentrated solar power (CSP) systems due to the facts that they are highly transparent, resistant to ultraviolet (UV) light and abrasion, and chemically inert. However, the reliable operation over long periods of outdoor exposure of such solar reflectors depends on the adequate adhesion between each layer to prevent delamination and subsequent failure. We report results from measurements of the delamination fracture energy (DFE) of the weakest interface in both as-deposited and aged reflectors, where the reflector construction consists of a glass/copper/silver/oxide stack. In this study, DFE was measured using a width-tapered beam method and the test results showed that the weakest interface of this solar reflector is the copper-glass interface, with a delamination fracture energy of approximately 4.4 J/m 2 . In order to verify the test results, finite element (FE) simulations were run using the commercial software package ABAQUS 6.14 based on the cohesive zone model (CZM). In the simulations, the DFE derived from the delamination measurement was treated as an input and the delamination forces from the FE simulations were compared to the experimental results. The good agreement between the tested and simulated delamination force indicated that this width-tapered beam method is accurate even for very small DFE, making it appropriate to test the DFE of front surfaced glass solar reflectors. Additionally, in order to study the aging effect on the DFE, accelerated aging tests were conducted using samples with different protective coatings, one group of samples with alumina ( Al 2 O 3 ) protective coating and the other group with titania ( TiO 2 ) protective coating. The DFE after 50 and 100 hours of accelerated aging were measured. The test results showed that the copper-glass interface would still be the weakest interface for all samples after aging, and the DFE for samples with Al 2 O 3 protective coating was unchanged whereas the copper-glass interface was found to undergo statistically significant change after both 50 and 100 hours of aging for samples with TiO 2 protective coating. We found that DFE at the copper/glass interface decreased after 50 hours of aging then increased after 100 hours of aging. The origin of this non-monotonic response of TiO 2 coated reflectors under accelerated aging conditions is unknown.

36 MATERIALS SCIENCE↗

A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

The Geant4 simulation toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models rely on measured cross-sections and phenomenological models with the physically motivated parameters that are tuned to cover many application domains. To study what uncertainties are associated with the Geant4 physics models we have designed and implemented a comprehensive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies. It also enables analysis of multiple variants of the resulting physics observables of interest in order to estimate the uncertainties associated with the simulation model choices. Based on modern event-processing infrastructure software, the toolkit offers a variety of attractive features, e.g. exible run-time con gurable work ow, comprehensive bookkeeping, easy to expand collection of analytical components. Design, implementation technology, and key functionalities of the toolkit are presented in this paper and illustrated with selected results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Peculiarities of highly burned-up NPP SNF reprocessing and new approach to simulation of solvent extraction processes

Substantiation, general description and performance characteristics of a reprocessing flowsheet for WWER-1000 spent fuel with burn-up >60 GW*day/t U is given. Pu and U losses were <0.1%, separation factor > 10{sup 4}; their decontamination factor from γ-emitting fission products was 4*10{sup 4} and 3*10{sup 7}, respectively. Zr, Tc, Np removal was >98% at U and Pu losses <0.05%. A new approach to simulation of extraction equilibrium has been developed. It is based on a set of simultaneous chemical reactions characterized by apparent concentration constants. A software package was created for simulation of spent fuel component distribution in multistage countercurrent extraction processes in the presence of salting out agents. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The Virtual Environment for Reactor Applications (VERA): Design and architecture

VERA, the Virtual Environment for Reactor Applications, is the system of physics capabilities being developed and deployed by the Consortium for Advanced Simulation of Light Water Reactors (CASL). CASL was established for the modeling and simulation of commercial nuclear reactors. VERA consists of integrating and interfacing software together with a suite of physics components adapted and/or refactored to simulate relevant physical phenomena in a coupled manner. VERA also includes the software development environment and computational infrastructure needed for these components to be effectively used. We describe the architecture of VERA from both software and numerical perspectives, along with the goals and constraints that drove major design decisions, and their implications. We explain why VERA is an environment rather than a framework or toolkit, why these distinctions are relevant (particularly for coupled physics applications), and provide an overview of results that demonstrate the use of VERA tools for a variety of challenging applications within the nuclear industry.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

h and hp -adaptive finite elements with local ALE for modeling turbulent reactive flow in engines with injection

LANL and our collaborators are facilitating the effort for predictive internal combustion engine modeling. We are developing an hp -adaptive finite element methods (FEM) software that provides a high degree of accuracy and solution robustness. This FEM projection method, a predictor-corrector scheme (PCS) has excellent capability over all flow regimes. The system is applicable to Newtonian and non-Newtonian fluids, turbulent reactive flows with sprays and using a new local ALE method for immersed moving parts. These algorithms are capable of representing the physics within an engine. T-3 and its collaborators provide software that many use directly for engine simulation or that they may alter with various models. KIVA software is in use worldwide by hundreds of Universities and dozens of corporations involved in research, engine design and manufacturing. We are working to deliver a more predictive capability to help in the understanding of combustion engines, thereby providing for greater efficiency and lower unwanted emissions.

02 PETROLEUM↗

Impact of Interface Recombination on Time Resolved Photoluminescence Decays (TRPL) in CdTe Solar Cells (Numerical Simulation Analysis) (Poster)

Using Sentaurus Device Software, we analyze how bulk and interface recombination affect time-resolved photoluminescence (TRPL) decays in CdTe solar cells. This modeling analysis could improve the interpretation of TRPL data and increase the possibility of rapid defect characterization in thin-film solar cells. By illuminating the samples with photons of two different wavelengths, we try to deducethe spatial origin of the dominant recombination loss. Shorter-wavelength photons will be more affected by the interface recombination and drift compared to the longer ones. Using the two-wavelength TRPL characterization method, it may be possible to determine whether a specific change in deposition process has affected the properties of interface or the bulk of the absorber.

14 SOLAR ENERGY↗

Developing an Automated Uncertainty Quantification Tool to Improve Watershed-Scale Predictions of Water and Nutrient Cycling

Managing the flow of water, nutrients, and contaminants in watersheds is vital to addressing pressing issues related to water scarcity, access to clean drinking water, energy production, resilience to natural and anthropogenic perturbations, and ecological restoration. Decisions about the management of watersheds critically depend on the accuracy with which the flow of water and chemicals through the watershed can be predicted by computer models. Prediction uncertainty can be reduced by matching the model to data, which are collected in the field at great expense. The contribution of watershed characterization data to reducing uncertainty of relevant model predictions can be evaluated in a so-called data-worth analysis, which provides transparent, quantitative metrics about a data set’s value for the support of relevant watershed management objectives. To achieve this goal, we developed a software package that implements the data-worth analysis approach for use with state-of-the-art watershed models. The purpose of the proposed data-worth analysis is to help decision-makers allocate resources for watershed characterization such that the uncertainty in model predictions can be significantly reduced, which leads to better, more effective management decisions. At the same time, watershed characterization costs can be reduced. The specific technical objectives of this SBIR/STTR Phase II project were to develop a framework and associated software toolsets that implement the uncertainty quantification and data-worth analysis approach for use with state-of-the-art watershed models. This goal was achieved by (A) developing a user-friendly, robust software package that is accessible to a wide audience, including watershed managers, policy-makers, and public stakeholders; (B) by demonstrating application of the prototype on several use cases that are representative of complex watershed management challenges spanning a range of scales and that consider different open-source, DOE-based codes and other modeling platforms; and (C) by gathering information about the needs and requirements from potential users to help guide future developments, ensuring that the final product will be commercially viable. The developed software consists of a graphical user interface that guides the user through a sequence of analysis steps, supported by toolsets that leverage state-of-the-art computational simulation-optimization capabilities. A prototype of the software runs on multiple platforms (PC, Mac, multi-processor Linux environment), is linked to diverse watershed simulators (e.g., ECOSYS, TOUGH2, TOUGHREACT, Amanzi-ATS), performs multiple analysis tasks (predictive simulations, sensitivity analysis, uncertainty analysis, automatic parameter estimation, and data-worth analysis, multicomponent geothermometry), and is readily extensible to include external simulators and analysis tools. The software is being commercialized and will be continually updated to address user needs.

58 GEOSCIENCES↗

Advanced Potential Energy Surfaces for Molecular Simulation

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). Here in this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. Finally, we have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Control And Optimization Modular Modeling Application For Nuclear Deployment

The purpose of the COMMAND code is to provide a flexible, scalable tool for use in developing, integrating, and testing the technologies necessary for achieving autonomous operations of advanced nuclear reactors. The code enables users to efficiently implement custom simulations and experiments by combining key methods from different software modules. These modules are focused on: modeling and simulation tools, such as nuclear simulation tools used for high-fidelity modeling (e.g., Reactor Excursion and Leak Analysis Program [RELAP5-3D] and Monte Carlo N-Particle [MCNP]); machine learning and optimization tools (e.g., anomaly detection and data-driven modeling techniques); advanced control in its digital, high-performance, and supervisory control forms (e.g., proportional integral derivative (PID) control and model predictive control (MPC); and integration with hardware through industrial communication protocols. To ensure flexibility and scalability, COMMAND was designed to be both modular—the software “pieces” all inherit from generic building blocks and can be combined and connected to create complicated simulations—and high performing—designed for parallel processing, enabling simulations and experiments to take advantage of multi-core computers, servers, and nodes. The code is written in the Python programming language due to the language's popularity, active community, and open-source and cross-platform nature. Maintaining consistency with other simulation tools used within the nuclear energy community, users implement simulations and experiments through text input files, which define components, parameters, connections, etc., through lines of text. Given that COMMAND is written in Python, these input files are native Python scripts, and so use the standard Python structure and formatting. This also enables users to take advantage of Python's extensive package library to develop custom capabilities for their specific use cases.

Faber, Jacob [Idaho National Laboratory (INL), Ida↗

Event-modeled Risk Assessment Using Linked Diagrams

In order to develop a dynamic probabilistic risk assessment capability, a prototype discrete event simulator was created as part of an LDRD that can model dynamic systems and generate probabilistic risk/reliability results. The development consisted of three major parts: 1. Development of a discrete event modeling software library 2. Design of a simulation object model for dynamic modeling 3. Construction of the graphical user interface (GUI) that will allow risk assessment analysts to more easily develop these models We called this new tool EMRALD. A key part of the EMRALD tool has been to develop an object-oriented software model that is flexible enough to support the varied dynamic simulation models (e.g., fails to operate, fails on demand). An object-oriented approach better matches the simulation model to real world objects and makes it more intuitive for the modeler. The interface represents actual physical components, specifically tracking how they interact. EMRALD is a discrete-event simulation tool that is coupled with a state-based diagramming graphical user interface. A key part of the EMRALD tool has been to develop an object-oriented software model that is flexible enough to support the varied dynamic simulation models (e.g., fails to operate, fails on demand). By having a state-based approach, we can integrate different hazards into a single comprehensive model. For example, a single model can include fire, flooding, transient, and seismic initiating events -- each of these events becomes a trigger into the state-based approach that tell the model to make a transition based upon the specific initiator. An object-oriented approach better matches the simulation model to real world objects and makes it more intuitive for the modeler. The interface represents actual physical components, specifically tracking how they interact.

Smith, CurtisLee↗

Hermes-3: Multi-component plasma simulations with BOUT++

A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. Hermes-3 is built on plasma simulation framework BOUT++, consolidating earlier SD1D and Hermes models into a single code that can be configured at run-time to solve plasma models in 1D, 2D or 3D, either for transport (steady-state) or turbulent (time-evolving) problems, with an arbitrary number of ion and neutral species. Here, we describe the improved numerical algorithms and software design that have been implemented in Hermes-3. To demonstrate the capabilities of this tool, applications relevant to the boundary of tokamak plasmas are presented: 1D simulations of diveror plasmas evolving equations for all charge states of neon and deuterium; 2D transport simulations of tokamak equilibria in single-null X-point geometry with plasma ion and neutral atom species; and simulations of the time-dependent propagation of plasma filaments (blobs). Hermes-3 is publicly available on Github under the GPL-3 open source license. The repository includes documentation and a suite of unit, integrated and convergence tests.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Pronghorn: A Porous Media Thermal-Hydraulics Core Simulator and its Validation with the SANA Experiments

Pebble bed High Temperature Reactors (HTRs) are characterized by many advantageous design features, such as excellent passive heat removal in accidents, large margins to fuel failure, and online refueling potential. However, a significant challenge in the core modeling of pebble bed reactors is the complex fuel-coolant structure. This paper presents a new porous media simulation code, Pronghorn, that aims to alleviate modeling challenges for pebble bed reactors by providing a fast-running, medium- fidelity core simulator. Pronghorn is intended to accelerate the design and analysis cycle for pebble bed and prismatic HTRs by permitting fast scoping studies and providing boundary conditions for systems-level analysis. Pronghorn is built on the Multiphysics Object-Oriented Simulation Environment (MOOSE) using modern software practices and a thorough testing framework. This paper describes the physical models used in Pronghorn and demonstrates Pronghorn’s capability for modeling gas-cooled pebble bed HTRs by presenting simulation results obtained for the German SANA pebble bed decay heat experiments. Within the limitations of the porous media approximation and existing available closure relationships, Pronghorn predicts the SANA experimental pebble temperatures well, expanding the code’s validation base. A brief code-to-code comparison shows a similar level of accuracy with other porous media simulation tools; this enhances Pronghorn’s advantages of an arbitrary equation of state, unstructured mesh capabilities, compressible flow models, high coupling potential to MOOSE fuels performance and systems-level thermal-hydraulics codes, and modern software design.

42 ENGINEERING↗

Analysis of DOE's Roof Savings Calculator with Comparison to other Simulation Engines

A web-based Roof Savings Calculator (RSC) has been deployed for the Department of Energy as an industry-consensus tool to help building owners, manufacturers, distributors, contractors and researchers easily run complex roof and attic simulations. This tool employs the latest web technologies and usability design to provide an easy input interface to an annual simulation of hour-by-hour, whole-building performance using the world-class simulation tools DOE-2.1E and AtticSim. Building defaults were assigned based on national averages and can provide estimated annual energy and cost savings after the user selects nothing more than building location. In addition to cool reflective roofs, the RSC tool can simulate multiple roof and attic configurations including different roof slopes, above sheathing ventilation, radiant barriers, low-emittance surfaces, HVAC duct location, duct leakage rates, multiple layers of building materials, ceiling and deck insulation levels, and other parameters. A base case and energy-efficient alternative can be compared side-by-side to generate an energy/cost savings estimate between two buildings. The RSC tool was benchmarked against field data for demonstration homes in Ft. Irwin, CA. However, RSC gives different energy savings estimates than previous cool roof simulation tools so more thorough software and empirical validation proved necessary. This report consolidates much of the preliminary analysis for comparison of RSC s projected energy savings to that from other simulation engines.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Refinery burner simulation design architecture summary.

This report describes the architectural design for a high fidelity simulation of a refinery and refinery burner, including demonstrations of impacts to the refinery if errors occur during the refinery process. The refinery burner model and simulation are a part of the capabilities within the Sandia National Laboratories Virtual Control System Environment (VCSE). Three components comprise the simulation: HMIs developed with commercial SCADA software, a PLC controller, and visualization software. All of these components run on different machines. This design, documented after the simulation development, incorporates aspects not traditionally seen in an architectural design, but that were utilized in this particular demonstration development. Key to the success of this model development and presented in this report are the concepts of the multiple aspects of model design and development that must be considered to capture the necessary model representation fidelity of the physical systems.

99 GENERAL AND MISCELLANEOUS↗

Parallel and Highly Innovative Simulation for INL Code System

The software is capable of performing: - Solution of neutron transport equations 1) using second order spherical harmonics and hybrid finite element or 2) using discrete ordinate and continuous finite element approach (INSTANT module) - Solve Bateman equation for an arbitrary number of isotopes (MRTAU module) - Solve time dependent transport equation using the INSTANT solver for the pseudo steady state equation - Provide power feedback to the RELAP5-3D code for nuclear reactor transient analysis - Provide cross section manipulation capability (interpolation, extraction, micro to macro)

Rabiti, Cristian↗

Verification of the Coupled Fluid/Solid Transfer in a CASL Grid-to-Rod-Fretting Simulation: A Technical Brief on the Analysis of Convergence Behavior and Demonstration of Software Tools for Verification

For a CASL grid-to-rod fretting problem, Sandia's Percept software was used in conjunction with the Sierra Mechanics suite to analyze the convergence behavior of the data transfer from a fluid simulation to a solid mechanics simulation. An analytic function, with properties relatively close to numerically computed fluid approximations, was chosen to represent the pressure solution in the fluid domain. The analytic pressure was interpolated on a sequence of grids on the fluid domain, and transferred onto a separate sequence of grids in the solid domain. The error in the resulting pressure in the solid domain was measured with respect to the analytic pressure. The error in pressure approached zero as both the fluid and solids meshes were refined. The convergence of the transfer algorithm was limited by whether the source grid resolution was the same or finer than the target grid resolution. In addition, using a feature coverage analysis, we found gaps in the solid mechanics code verification test suite directly relevant to the prototype CASL GTRF simulations.

99 GENERAL AND MISCELLANEOUS↗