Towards Systematic Benchmarking of Climate Model Performance

NASA Astrophysics Data System (ADS)

Gleckler, P. J.

2014-12-01

The process by which climate models are evaluated has evolved substantially over the past decade, with the Coupled Model Intercomparison Project (CMIP) serving as a centralizing activity for coordinating model experimentation and enabling research. Scientists with a broad spectrum of expertise have contributed to the CMIP model evaluation process, resulting in many hundreds of publications that have served as a key resource for the IPCC process. For several reasons, efforts are now underway to further systematize some aspects of the model evaluation process. First, some model evaluation can now be considered routine and should not require "re-inventing the wheel" or a journal publication simply to update results with newer models. Second, the benefit of CMIP research to model development has not been optimal because the publication of results generally takes several years and is usually not reproducible for benchmarking newer model versions. And third, there are now hundreds of model versions and many thousands of simulations, but there is no community-based mechanism for routinely monitoring model performance changes. An important change in the design of CMIP6 can help address these limitations. CMIP6 will include a small set standardized experiments as an ongoing exercise (CMIP "DECK": ongoing Diagnostic, Evaluation and Characterization of Klima), so that modeling groups can submit them at any time and not be overly constrained by deadlines. In this presentation, efforts to establish routine benchmarking of existing and future CMIP simulations will be described. To date, some benchmarking tools have been made available to all CMIP modeling groups to enable them to readily compare with CMIP5 simulations during the model development process. A natural extension of this effort is to make results from all CMIP simulations widely available, including the results from newer models as soon as the simulations become available for research. Making the results from routine performance tests readily accessible will help advance a more transparent model evaluation process.

Computers for real time flight simulation: A market survey

NASA Technical Reports Server (NTRS)

Bekey, G. A.; Karplus, W. J.

1977-01-01

An extensive computer market survey was made to determine those available systems suitable for current and future flight simulation studies at Ames Research Center. The primary requirement is for the computation of relatively high frequency content (5 Hz) math models representing powered lift flight vehicles. The Rotor Systems Research Aircraft (RSRA) was used as a benchmark vehicle for computation comparison studies. The general nature of helicopter simulations and a description of the benchmark model are presented, and some of the sources of simulation difficulties are examined. A description of various applicable computer architectures is presented, along with detailed discussions of leading candidate systems and comparisons between them.

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

Assessment of Static Delamination Propagation Capabilities in Commercial Finite Element Codes Using Benchmark Analysis

NASA Technical Reports Server (NTRS)

Orifici, Adrian C.; Krueger, Ronald

2010-01-01

With capabilities for simulating delamination growth in composite materials becoming available, the need for benchmarking and assessing these capabilities is critical. In this study, benchmark analyses were performed to assess the delamination propagation simulation capabilities of the VCCT implementations in Marc TM and MD NastranTM. Benchmark delamination growth results for Double Cantilever Beam, Single Leg Bending and End Notched Flexure specimens were generated using a numerical approach. This numerical approach was developed previously, and involves comparing results from a series of analyses at different delamination lengths to a single analysis with automatic crack propagation. Specimens were analyzed with three-dimensional and two-dimensional models, and compared with previous analyses using Abaqus . The results demonstrated that the VCCT implementation in Marc TM and MD Nastran(TradeMark) was capable of accurately replicating the benchmark delamination growth results and that the use of the numerical benchmarks offers advantages over benchmarking using experimental and analytical results.

An Enriched Shell Element for Delamination Simulation in Composite Laminates

NASA Technical Reports Server (NTRS)

McElroy, Mark

2015-01-01

A formulation is presented for an enriched shell finite element capable of delamination simulation in composite laminates. The element uses an adaptive splitting approach for damage characterization that allows for straightforward low-fidelity model creation and a numerically efficient solution. The Floating Node Method is used in conjunction with the Virtual Crack Closure Technique to predict delamination growth and represent it discretely at an arbitrary ply interface. The enriched element is verified for Mode I delamination simulation using numerical benchmark data. After determining important mesh configuration guidelines for the vicinity of the delamination front in the model, a good correlation was found between the enriched shell element model results and the benchmark data set.

Benchmark Evaluation of Start-Up and Zero-Power Measurements at the High-Temperature Engineering Test Reactor

DOE PAGES

Bess, John D.; Fujimoto, Nozomu

2014-10-09

Benchmark models were developed to evaluate six cold-critical and two warm-critical, zero-power measurements of the HTTR. Additional measurements of a fully-loaded subcritical configuration, core excess reactivity, shutdown margins, six isothermal temperature coefficients, and axial reaction-rate distributions were also evaluated as acceptable benchmark experiments. Insufficient information is publicly available to develop finely-detailed models of the HTTR as much of the design information is still proprietary. However, the uncertainties in the benchmark models are judged to be of sufficient magnitude to encompass any biases and bias uncertainties incurred through the simplification process used to develop the benchmark models. Dominant uncertainties in themore » experimental keff for all core configurations come from uncertainties in the impurity content of the various graphite blocks that comprise the HTTR. Monte Carlo calculations of keff are between approximately 0.9 % and 2.7 % greater than the benchmark values. Reevaluation of the HTTR models as additional information becomes available could improve the quality of this benchmark and possibly reduce the computational biases. High-quality characterization of graphite impurities would significantly improve the quality of the HTTR benchmark assessment. Simulation of the other reactor physics measurements are in good agreement with the benchmark experiment values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments.« less

Surrogate model approach for improving the performance of reactive transport simulations

NASA Astrophysics Data System (ADS)

Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris

2016-04-01

Reactive transport models can serve a large number of important geoscientific applications involving underground resources in industry and scientific research. It is common for simulation of reactive transport to consist of at least two coupled simulation models. First is a hydrodynamics simulator that is responsible for simulating the flow of groundwaters and transport of solutes. Hydrodynamics simulators are well established technology and can be very efficient. When hydrodynamics simulations are performed without coupled geochemistry, their spatial geometries can span millions of elements even when running on desktop workstations. Second is a geochemical simulation model that is coupled to the hydrodynamics simulator. Geochemical simulation models are much more computationally costly. This is a problem that makes reactive transport simulations spanning millions of spatial elements very difficult to achieve. To address this problem we propose to replace the coupled geochemical simulation model with a surrogate model. A surrogate is a statistical model created to include only the necessary subset of simulator complexity for a particular scenario. To demonstrate the viability of such an approach we tested it on a popular reactive transport benchmark problem that involves 1D Calcite transport. This is a published benchmark problem (Kolditz, 2012) for simulation models and for this reason we use it to test the surrogate model approach. To do this we tried a number of statistical models available through the caret and DiceEval packages for R, to be used as surrogate models. These were trained on randomly sampled subset of the input-output data from the geochemical simulation model used in the original reactive transport simulation. For validation we use the surrogate model to predict the simulator output using the part of sampled input data that was not used for training the statistical model. For this scenario we find that the multivariate adaptive regression splines (MARS) method provides the best trade-off between speed and accuracy. This proof-of-concept forms an essential step towards building an interactive visual analytics system to enable user-driven systematic creation of geochemical surrogate models. Such a system shall enable reactive transport simulations with unprecedented spatial and temporal detail to become possible. References: Kolditz, O., Görke, U.J., Shao, H. and Wang, W., 2012. Thermo-hydro-mechanical-chemical processes in porous media: benchmarks and examples (Vol. 86). Springer Science & Business Media.

Benchmarking computational fluid dynamics models of lava flow simulation for hazard assessment, forecasting, and risk management

USGS Publications Warehouse

Dietterich, Hannah; Lev, Einat; Chen, Jiangzhi; Richardson, Jacob A.; Cashman, Katharine V.

2017-01-01

Numerical simulations of lava flow emplacement are valuable for assessing lava flow hazards, forecasting active flows, designing flow mitigation measures, interpreting past eruptions, and understanding the controls on lava flow behavior. Existing lava flow models vary in simplifying assumptions, physics, dimensionality, and the degree to which they have been validated against analytical solutions, experiments, and natural observations. In order to assess existing models and guide the development of new codes, we conduct a benchmarking study of computational fluid dynamics (CFD) models for lava flow emplacement, including VolcFlow, OpenFOAM, FLOW-3D, COMSOL, and MOLASSES. We model viscous, cooling, and solidifying flows over horizontal planes, sloping surfaces, and into topographic obstacles. We compare model results to physical observations made during well-controlled analogue and molten basalt experiments, and to analytical theory when available. Overall, the models accurately simulate viscous flow with some variability in flow thickness where flows intersect obstacles. OpenFOAM, COMSOL, and FLOW-3D can each reproduce experimental measurements of cooling viscous flows, and OpenFOAM and FLOW-3D simulations with temperature-dependent rheology match results from molten basalt experiments. We assess the goodness-of-fit of the simulation results and the computational cost. Our results guide the selection of numerical simulation codes for different applications, including inferring emplacement conditions of past lava flows, modeling the temporal evolution of ongoing flows during eruption, and probabilistic assessment of lava flow hazard prior to eruption. Finally, we outline potential experiments and desired key observational data from future flows that would extend existing benchmarking data sets.

Global Gridded Crop Model Evaluation: Benchmarking, Skills, Deficiencies and Implications.

NASA Technical Reports Server (NTRS)

Muller, Christoph; Elliott, Joshua; Chryssanthacopoulos, James; Arneth, Almut; Balkovic, Juraj; Ciais, Philippe; Deryng, Delphine; Folberth, Christian; Glotter, Michael; Hoek, Steven;

Benchmark simulation Model no 2 in Matlab-simulink: towards plant-wide WWTP control strategy evaluation.

PubMed

Vreck, D; Gernaey, K V; Rosen, C; Jeppsson, U

2006-01-01

In this paper, implementation of the Benchmark Simulation Model No 2 (BSM2) within Matlab-Simulink is presented. The BSM2 is developed for plant-wide WWTP control strategy evaluation on a long-term basis. It consists of a pre-treatment process, an activated sludge process and sludge treatment processes. Extended evaluation criteria are proposed for plant-wide control strategy assessment. Default open-loop and closed-loop strategies are also proposed to be used as references with which to compare other control strategies. Simulations indicate that the BM2 is an appropriate tool for plant-wide control strategy evaluation.

Implementing ADM1 for plant-wide benchmark simulations in Matlab/Simulink.

PubMed

Rosen, C; Vrecko, D; Gernaey, K V; Pons, M N; Jeppsson, U

2006-01-01

The IWA Anaerobic Digestion Model No.1 (ADM1) was presented in 2002 and is expected to represent the state-of-the-art model within this field in the future. Due to its complexity the implementation of the model is not a simple task and several computational aspects need to be considered, in particular if the ADM1 is to be included in dynamic simulations of plant-wide or even integrated systems. In this paper, the experiences gained from a Matlab/Simulink implementation of ADM1 into the extended COST/IWA Benchmark Simulation Model (BSM2) are presented. Aspects related to system stiffness, model interfacing with the ASM family, mass balances, acid-base equilibrium and algebraic solvers for pH and other troublesome state variables, numerical solvers and simulation time are discussed. The main conclusion is that if implemented properly, the ADM1 will also produce high-quality results in dynamic plant-wide simulations including noise, discrete sub-systems, etc. without imposing any major restrictions due to extensive computational efforts.

A Modular Simulation Framework for Assessing Swarm Search Models

DTIC Science & Technology

2014-09-01

SUBTITLE A MODULAR SIMULATION FRAMEWORK FOR ASSESSING SWARM SEARCH MODELS 5. FUNDING NUMBERS 6. AUTHOR(S) Blake M. Wanier 7. PERFORMING ORGANIZATION...Numerical studies demonstrate the ability to leverage the developed simulation and analysis framework to investigate three canonical swarm search models ...as benchmarks for future exploration of more sophisticated swarm search scenarios. 14. SUBJECT TERMS Swarm Search, Search Theory, Modeling Framework

Benchmarking FEniCS for mantle convection simulations

NASA Astrophysics Data System (ADS)

Vynnytska, L.; Rognes, M. E.; Clark, S. R.

2013-01-01

This paper evaluates the usability of the FEniCS Project for mantle convection simulations by numerical comparison to three established benchmarks. The benchmark problems all concern convection processes in an incompressible fluid induced by temperature or composition variations, and cover three cases: (i) steady-state convection with depth- and temperature-dependent viscosity, (ii) time-dependent convection with constant viscosity and internal heating, and (iii) a Rayleigh-Taylor instability. These problems are modeled by the Stokes equations for the fluid and advection-diffusion equations for the temperature and composition. The FEniCS Project provides a novel platform for the automated solution of differential equations by finite element methods. In particular, it offers a significant flexibility with regard to modeling and numerical discretization choices; we have here used a discontinuous Galerkin method for the numerical solution of the advection-diffusion equations. Our numerical results are in agreement with the benchmarks, and demonstrate the applicability of both the discontinuous Galerkin method and FEniCS for such applications.

Humidification of Blow-By Oxygen During Recovery of Postoperative Pediatric Patients: One Unit's Journey.

PubMed

Donahue, Suzanne; DiBlasi, Robert M; Thomas, Karen

2018-02-02

To examine the practice of nebulizer cool mist blow-by oxygen administered to spontaneously breathing postanesthesia care unit (PACU) pediatric patients during Phase one recovery. Existing evidence was evaluated. Informal benchmarking documented practices in peer organizations. An in vitro study was then conducted to simulate clinical practice and determine depth and amount of airway humidity delivery with blow-by oxygen. Informal benchmarking information was obtained by telephone interview. Using a three-dimensional printed simulation model of the head connected to a breathing lung simulator, depth and amount of moisture delivery in the respiratory tree were measured. Evidence specific to PACU administration of cool mist blow-by oxygen was limited. Informal benchmarking revealed that routine cool mist oxygenated blow-by administration was not widely practiced. The laboratory experiment revealed minimal moisture reaching the mid-tracheal area of the simulated airway model. Routine use of oxygenated cool mist in spontaneously breathing pediatric PACU patients is not supported. Copyright © 2017 American Society of PeriAnesthesia Nurses. Published by Elsevier Inc. All rights reserved.

Evaluation of Neutron Radiography Reactor LEU-Core Start-Up Measurements

DOE PAGES

Bess, John D.; Maddock, Thomas L.; Smolinski, Andrew T.; ...

2014-11-04

Benchmark models were developed to evaluate the cold-critical start-up measurements performed during the fresh core reload of the Neutron Radiography (NRAD) reactor with Low Enriched Uranium (LEU) fuel. Experiments include criticality, control-rod worth measurements, shutdown margin, and excess reactivity for four core loadings with 56, 60, 62, and 64 fuel elements. The worth of four graphite reflector block assemblies and an empty dry tube used for experiment irradiations were also measured and evaluated for the 60-fuel-element core configuration. Dominant uncertainties in the experimental k eff come from uncertainties in the manganese content and impurities in the stainless steel fuel claddingmore » as well as the 236U and erbium poison content in the fuel matrix. Calculations with MCNP5 and ENDF/B-VII.0 neutron nuclear data are approximately 1.4% (9σ) greater than the benchmark model eigenvalues, which is commonly seen in Monte Carlo simulations of other TRIGA reactors. Simulations of the worth measurements are within the 2σ uncertainty for most of the benchmark experiment worth values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments.« less

Evaluation of Neutron Radiography Reactor LEU-Core Start-Up Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bess, John D.; Maddock, Thomas L.; Smolinski, Andrew T.

Benchmark models were developed to evaluate the cold-critical start-up measurements performed during the fresh core reload of the Neutron Radiography (NRAD) reactor with Low Enriched Uranium (LEU) fuel. Experiments include criticality, control-rod worth measurements, shutdown margin, and excess reactivity for four core loadings with 56, 60, 62, and 64 fuel elements. The worth of four graphite reflector block assemblies and an empty dry tube used for experiment irradiations were also measured and evaluated for the 60-fuel-element core configuration. Dominant uncertainties in the experimental k eff come from uncertainties in the manganese content and impurities in the stainless steel fuel claddingmore » as well as the 236U and erbium poison content in the fuel matrix. Calculations with MCNP5 and ENDF/B-VII.0 neutron nuclear data are approximately 1.4% (9σ) greater than the benchmark model eigenvalues, which is commonly seen in Monte Carlo simulations of other TRIGA reactors. Simulations of the worth measurements are within the 2σ uncertainty for most of the benchmark experiment worth values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments.« less

INL Results for Phases I and III of the OECD/NEA MHTGR-350 Benchmark

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerhard Strydom; Javier Ortensi; Sonat Sen

2013-09-01

The Idaho National Laboratory (INL) Very High Temperature Reactor (VHTR) Technology Development Office (TDO) Methods Core Simulation group led the construction of the Organization for Economic Cooperation and Development (OECD) Modular High Temperature Reactor (MHTGR) 350 MW benchmark for comparing and evaluating prismatic VHTR analysis codes. The benchmark is sponsored by the OECD's Nuclear Energy Agency (NEA), and the project will yield a set of reference steady-state, transient, and lattice depletion problems that can be used by the Department of Energy (DOE), the Nuclear Regulatory Commission (NRC), and vendors to assess their code suits. The Methods group is responsible formore » defining the benchmark specifications, leading the data collection and comparison activities, and chairing the annual technical workshops. This report summarizes the latest INL results for Phase I (steady state) and Phase III (lattice depletion) of the benchmark. The INSTANT, Pronghorn and RattleSnake codes were used for the standalone core neutronics modeling of Exercise 1, and the results obtained from these codes are compared in Section 4. Exercise 2 of Phase I requires the standalone steady-state thermal fluids modeling of the MHTGR-350 design, and the results for the systems code RELAP5-3D are discussed in Section 5. The coupled neutronics and thermal fluids steady-state solution for Exercise 3 are reported in Section 6, utilizing the newly developed Parallel and Highly Innovative Simulation for INL Code System (PHISICS)/RELAP5-3D code suit. Finally, the lattice depletion models and results obtained for Phase III are compared in Section 7. The MHTGR-350 benchmark proved to be a challenging simulation set of problems to model accurately, and even with the simplifications introduced in the benchmark specification this activity is an important step in the code-to-code verification of modern prismatic VHTR codes. A final OECD/NEA comparison report will compare the Phase I and III results of all other international participants in 2014, while the remaining Phase II transient case results will be reported in 2015.« less

Delay Tolerant Networking - Bundle Protocol Simulation

NASA Technical Reports Server (NTRS)

SeGui, John; Jenning, Esther

2006-01-01

In this paper, we report on the addition of MACHETE models needed to support DTN, namely: the Bundle Protocol (BP) model. To illustrate the useof MACHETE with the additional DTN model, we provide an example simulation to benchmark its performance. We demonstrate the use of the DTN protocol and discuss statistics gathered concerning the total time needed to simulate numerous bundle transmissions.

Experimental benchmark of kinetic simulations of capacitively coupled plasmas in molecular gases

NASA Astrophysics Data System (ADS)

Donkó, Z.; Derzsi, A.; Korolov, I.; Hartmann, P.; Brandt, S.; Schulze, J.; Berger, B.; Koepke, M.; Bruneau, B.; Johnson, E.; Lafleur, T.; Booth, J.-P.; Gibson, A. R.; O'Connell, D.; Gans, T.

2018-01-01

We discuss the origin of uncertainties in the results of numerical simulations of low-temperature plasma sources, focusing on capacitively coupled plasmas. These sources can be operated in various gases/gas mixtures, over a wide domain of excitation frequency, voltage, and gas pressure. At low pressures, the non-equilibrium character of the charged particle transport prevails and particle-based simulations become the primary tools for their numerical description. The particle-in-cell method, complemented with Monte Carlo type description of collision processes, is a well-established approach for this purpose. Codes based on this technique have been developed by several authors/groups, and have been benchmarked with each other in some cases. Such benchmarking demonstrates the correctness of the codes, but the underlying physical model remains unvalidated. This is a key point, as this model should ideally account for all important plasma chemical reactions as well as for the plasma-surface interaction via including specific surface reaction coefficients (electron yields, sticking coefficients, etc). In order to test the models rigorously, comparison with experimental ‘benchmark data’ is necessary. Examples will be given regarding the studies of electron power absorption modes in O2, and CF4-Ar discharges, as well as on the effect of modifications of the parameters of certain elementary processes on the computed discharge characteristics in O2 capacitively coupled plasmas.

A wind energy benchmark for ABL modelling of a diurnal cycle with a nocturnal low-level jet: GABLS3 revisited

DOE PAGES

Rodrigo, J. Sanz; Churchfield, M.; Kosović, B.

2016-10-03

The third GEWEX Atmospheric Boundary Layer Studies (GABLS3) model intercomparison study, around the Cabauw met tower in the Netherlands, is revisited as a benchmark for wind energy atmospheric boundary layer (ABL) models. The case was originally developed by the boundary layer meteorology community, interested in analysing the performance of single-column and large-eddy simulation atmospheric models dealing with a diurnal cycle leading to the development of a nocturnal low-level jet. The case addresses fundamental questions related to the definition of the large-scale forcing, the interaction of the ABL with the surface and the evaluation of model results with observations. The characterizationmore » of mesoscale forcing for asynchronous microscale modelling of the ABL is discussed based on momentum budget analysis of WRF simulations. Then a single-column model is used to demonstrate the added value of incorporating different forcing mechanisms in microscale models. The simulations are evaluated in terms of wind energy quantities of interest.« less

A suite of benchmark and challenge problems for enhanced geothermal systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Mark; Fu, Pengcheng; McClure, Mark

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulation capabilitiesmore » to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The problems involved two phases of research, stimulation, development, and circulation in two separate reservoirs. The challenge problems had specific questions to be answered via numerical simulation in three topical areas: 1) reservoir creation/stimulation, 2) reactive and passive transport, and 3) thermal recovery. Whereas the benchmark class of problems were designed to test capabilities for modeling coupled processes under strictly specified conditions, the stated objective for the challenge class of problems was to demonstrate what new understanding of the Fenton Hill experiments could be realized via the application of modern numerical simulation tools by recognized expert practitioners. We present the suite of benchmark and challenge problems developed for the GTO-CCS, providing problem descriptions and sample solutions.« less

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

How well does your model capture the terrestrial ecosystem dynamics of the Arctic-Boreal Region?

NASA Astrophysics Data System (ADS)

Stofferahn, E.; Fisher, J. B.; Hayes, D. J.; Huntzinger, D. N.; Schwalm, C.

2016-12-01

The Arctic-Boreal Region (ABR) is a major source of uncertainties for terrestrial biosphere model (TBM) simulations. These uncertainties are precipitated by a lack of observational data from the region, affecting the parameterizations of cold environment processes in the models. Addressing these uncertainties requires a coordinated effort of data collection and integration of the following key indicators of the ABR ecosystem: disturbance, flora / fauna and related ecosystem function, carbon pools and biogeochemistry, permafrost, and hydrology. We are developing a model-data integration framework for NASA's Arctic Boreal Vulnerability Experiment (ABoVE), wherein data collection for the key ABoVE indicators is driven by matching observations and model outputs to the ABoVE indicators. The data are used as reference datasets for a benchmarking system which evaluates TBM performance with respect to ABR processes. The benchmarking system utilizes performance metrics to identify intra-model and inter-model strengths and weaknesses, which in turn provides guidance to model development teams for reducing uncertainties in TBM simulations of the ABR. The system is directly connected to the International Land Model Benchmarking (ILaMB) system, as an ABR-focused application.

A new numerical benchmark for variably saturated variable-density flow and transport in porous media

NASA Astrophysics Data System (ADS)

Guevara, Carlos; Graf, Thomas

2016-04-01

In subsurface hydrological systems, spatial and temporal variations in solute concentration and/or temperature may affect fluid density and viscosity. These variations could lead to potentially unstable situations, in which a dense fluid overlies a less dense fluid. These situations could produce instabilities that appear as dense plume fingers migrating downwards counteracted by vertical upwards flow of freshwater (Simmons et al., Transp. Porous Medium, 2002). As a result of unstable variable-density flow, solute transport rates are increased over large distances and times as compared to constant-density flow. The numerical simulation of variable-density flow in saturated and unsaturated media requires corresponding benchmark problems against which a computer model is validated (Diersch and Kolditz, Adv. Water Resour, 2002). Recorded data from a laboratory-scale experiment of variable-density flow and solute transport in saturated and unsaturated porous media (Simmons et al., Transp. Porous Medium, 2002) is used to define a new numerical benchmark. The HydroGeoSphere code (Therrien et al., 2004) coupled with PEST (www.pesthomepage.org) are used to obtain an optimized parameter set capable of adequately representing the data set by Simmons et al., (2002). Fingering in the numerical model is triggered using random hydraulic conductivity fields. Due to the inherent randomness, a large number of simulations were conducted in this study. The optimized benchmark model adequately predicts the plume behavior and the fate of solutes. This benchmark is useful for model verification of variable-density flow problems in saturated and/or unsaturated media.

A chemical EOR benchmark study of different reservoir simulators

NASA Astrophysics Data System (ADS)

Goudarzi, Ali; Delshad, Mojdeh; Sepehrnoori, Kamy

2016-09-01

Interest in chemical EOR processes has intensified in recent years due to the advancements in chemical formulations and injection techniques. Injecting Polymer (P), surfactant/polymer (SP), and alkaline/surfactant/polymer (ASP) are techniques for improving sweep and displacement efficiencies with the aim of improving oil production in both secondary and tertiary floods. There has been great interest in chemical flooding recently for different challenging situations. These include high temperature reservoirs, formations with extreme salinity and hardness, naturally fractured carbonates, and sandstone reservoirs with heavy and viscous crude oils. More oil reservoirs are reaching maturity where secondary polymer floods and tertiary surfactant methods have become increasingly important. This significance has added to the industry's interest in using reservoir simulators as tools for reservoir evaluation and management to minimize costs and increase the process efficiency. Reservoir simulators with special features are needed to represent coupled chemical and physical processes present in chemical EOR processes. The simulators need to be first validated against well controlled lab and pilot scale experiments to reliably predict the full field implementations. The available data from laboratory scale include 1) phase behavior and rheological data; and 2) results of secondary and tertiary coreflood experiments for P, SP, and ASP floods under reservoir conditions, i.e. chemical retentions, pressure drop, and oil recovery. Data collected from corefloods are used as benchmark tests comparing numerical reservoir simulators with chemical EOR modeling capabilities such as STARS of CMG, ECLIPSE-100 of Schlumberger, REVEAL of Petroleum Experts. The research UTCHEM simulator from The University of Texas at Austin is also included since it has been the benchmark for chemical flooding simulation for over 25 years. The results of this benchmark comparison will be utilized to improve chemical design for field-scale studies using commercial simulators. The benchmark tests illustrate the potential of commercial simulators for chemical flooding projects and provide a comprehensive table of strengths and limitations of each simulator for a given chemical EOR process. Mechanistic simulations of chemical EOR processes will provide predictive capability and can aid in optimization of the field injection projects. The objective of this paper is not to compare the computational efficiency and solution algorithms; it only focuses on the process modeling comparison.

Finite Element Modeling of the World Federation's Second MFL Benchmark Problem

NASA Astrophysics Data System (ADS)

Zeng, Zhiwei; Tian, Yong; Udpa, Satish; Udpa, Lalita

2004-02-01

This paper presents results obtained by simulating the second magnetic flux leakage benchmark problem proposed by the World Federation of NDE Centers. The geometry consists of notches machined on the internal and external surfaces of a rotating steel pipe that is placed between two yokes that are part of a magnetic circuit energized by an electromagnet. The model calculates the radial component of the leaked field at specific positions. The nonlinear material property of the ferromagnetic pipe is taken into account in simulating the problem. The velocity effect caused by the rotation of the pipe is, however, ignored for reasons of simplicity.

Field Test of a Hybrid Finite-Difference and Analytic Element Regional Model.

PubMed

Abrams, D B; Haitjema, H M; Feinstein, D T; Hunt, R J

2016-01-01

Regional finite-difference models often have cell sizes that are too large to sufficiently model well-stream interactions. Here, a steady-state hybrid model is applied whereby the upper layer or layers of a coarse MODFLOW model are replaced by the analytic element model GFLOW, which represents surface waters and wells as line and point sinks. The two models are coupled by transferring cell-by-cell leakage obtained from the original MODFLOW model to the bottom of the GFLOW model. A real-world test of the hybrid model approach is applied on a subdomain of an existing model of the Lake Michigan Basin. The original (coarse) MODFLOW model consists of six layers, the top four of which are aggregated into GFLOW as a single layer, while the bottom two layers remain part of MODFLOW in the hybrid model. The hybrid model and a refined "benchmark" MODFLOW model simulate similar baseflows. The hybrid and benchmark models also simulate similar baseflow reductions due to nearby pumping when the well is located within the layers represented by GFLOW. However, the benchmark model requires refinement of the model grid in the local area of interest, while the hybrid approach uses a gridless top layer and is thus unaffected by grid discretization errors. The hybrid approach is well suited to facilitate cost-effective retrofitting of existing coarse grid MODFLOW models commonly used for regional studies because it leverages the strengths of both finite-difference and analytic element methods for predictions in mildly heterogeneous systems that can be simulated with steady-state conditions. © 2015, National Ground Water Association.

A Benchmarking Initiative for Reactive Transport Modeling Applied to Subsurface Environmental Applications

NASA Astrophysics Data System (ADS)

Steefel, C. I.

2015-12-01

Over the last 20 years, we have seen the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface environmental applications it is being used to address. Reactive transport modeling is being asked to provide accurate assessments of engineering performance and risk for important issues with far-reaching consequences. As a result, the complexity and detail of subsurface processes, properties, and conditions that can be simulated have significantly expanded. Closed form solutions are necessary and useful, but limited to situations that are far simpler than typical applications that combine many physical and chemical processes, in many cases in coupled form. In the absence of closed form and yet realistic solutions for complex applications, numerical benchmark problems with an accepted set of results will be indispensable to qualifying codes for various environmental applications. The intent of this benchmarking exercise, now underway for more than five years, is to develop and publish a set of well-described benchmark problems that can be used to demonstrate simulator conformance with norms established by the subsurface science and engineering community. The objective is not to verify this or that specific code--the reactive transport codes play a supporting role in this regard—but rather to use the codes to verify that a common solution of the problem can be achieved. Thus, the objective of each of the manuscripts is to present an environmentally-relevant benchmark problem that tests the conceptual model capabilities, numerical implementation, process coupling, and accuracy. The benchmark problems developed to date include 1) microbially-mediated reactions, 2) isotopes, 3) multi-component diffusion, 4) uranium fate and transport, 5) metal mobility in mining affected systems, and 6) waste repositories and related aspects.

Intercomparison of Monte Carlo radiation transport codes to model TEPC response in low-energy neutron and gamma-ray fields.

PubMed

Ali, F; Waker, A J; Waller, E J

2014-10-01

Tissue-equivalent proportional counters (TEPC) can potentially be used as a portable and personal dosemeter in mixed neutron and gamma-ray fields, but what hinders this use is their typically large physical size. To formulate compact TEPC designs, the use of a Monte Carlo transport code is necessary to predict the performance of compact designs in these fields. To perform this modelling, three candidate codes were assessed: MCNPX 2.7.E, FLUKA 2011.2 and PHITS 2.24. In each code, benchmark simulations were performed involving the irradiation of a 5-in. TEPC with monoenergetic neutron fields and a 4-in. wall-less TEPC with monoenergetic gamma-ray fields. The frequency and dose mean lineal energies and dose distributions calculated from each code were compared with experimentally determined data. For the neutron benchmark simulations, PHITS produces data closest to the experimental values and for the gamma-ray benchmark simulations, FLUKA yields data closest to the experimentally determined quantities. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Computer simulation to predict energy use, greenhouse gas emissions and costs for production of fluid milk using alternative processing methods

USDA-ARS?s Scientific Manuscript database

Computer simulation is a useful tool for benchmarking the electrical and fuel energy consumption and water use in a fluid milk plant. In this study, a computer simulation model of the fluid milk process based on high temperature short time (HTST) pasteurization was extended to include models for pr...

Benchmarking of neutron production of heavy-ion transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

Integral Full Core Multi-Physics PWR Benchmark with Measured Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forget, Benoit; Smith, Kord; Kumar, Shikhar

In recent years, the importance of modeling and simulation has been highlighted extensively in the DOE research portfolio with concrete examples in nuclear engineering with the CASL and NEAMS programs. These research efforts and similar efforts worldwide aim at the development of high-fidelity multi-physics analysis tools for the simulation of current and next-generation nuclear power reactors. Like all analysis tools, verification and validation is essential to guarantee proper functioning of the software and methods employed. The current approach relies mainly on the validation of single physic phenomena (e.g. critical experiment, flow loops, etc.) and there is a lack of relevantmore » multiphysics benchmark measurements that are necessary to validate high-fidelity methods being developed today. This work introduces a new multi-cycle full-core Pressurized Water Reactor (PWR) depletion benchmark based on two operational cycles of a commercial nuclear power plant that provides a detailed description of fuel assemblies, burnable absorbers, in-core fission detectors, core loading and re-loading patterns. This benchmark enables analysts to develop extremely detailed reactor core models that can be used for testing and validation of coupled neutron transport, thermal-hydraulics, and fuel isotopic depletion. The benchmark also provides measured reactor data for Hot Zero Power (HZP) physics tests, boron letdown curves, and three-dimensional in-core flux maps from 58 instrumented assemblies. The benchmark description is now available online and has been used by many groups. However, much work remains to be done on the quantification of uncertainties and modeling sensitivities. This work aims to address these deficiencies and make this benchmark a true non-proprietary international benchmark for the validation of high-fidelity tools. This report details the BEAVRS uncertainty quantification for the first two cycle of operations and serves as the final report of the project.« less

Benchmark simulation model no 2: general protocol and exploratory case studies.

PubMed

Jeppsson, U; Pons, M-N; Nopens, I; Alex, J; Copp, J B; Gernaey, K V; Rosen, C; Steyer, J-P; Vanrolleghem, P A

2007-01-01

Over a decade ago, the concept of objectively evaluating the performance of control strategies by simulating them using a standard model implementation was introduced for activated sludge wastewater treatment plants. The resulting Benchmark Simulation Model No 1 (BSM1) has been the basis for a significant new development that is reported on here: Rather than only evaluating control strategies at the level of the activated sludge unit (bioreactors and secondary clarifier) the new BSM2 now allows the evaluation of control strategies at the level of the whole plant, including primary clarifier and sludge treatment with anaerobic sludge digestion. In this contribution, the decisions that have been made over the past three years regarding the models used within the BSM2 are presented and argued, with particular emphasis on the ADM1 description of the digester, the interfaces between activated sludge and digester models, the included temperature dependencies and the reject water storage. BSM2-implementations are now available in a wide range of simulation platforms and a ring test has verified their proper implementation, consistent with the BSM2 definition. This guarantees that users can focus on the control strategy evaluation rather than on modelling issues. Finally, for illustration, twelve simple operational strategies have been implemented in BSM2 and their performance evaluated. Results show that it is an interesting control engineering challenge to further improve the performance of the BSM2 plant (which is the whole idea behind benchmarking) and that integrated control (i.e. acting at different places in the whole plant) is certainly worthwhile to achieve overall improvement.

Benchmarking urban flood models of varying complexity and scale using high resolution terrestrial LiDAR data

NASA Astrophysics Data System (ADS)

Fewtrell, Timothy J.; Duncan, Alastair; Sampson, Christopher C.; Neal, Jeffrey C.; Bates, Paul D.

2011-01-01

This paper describes benchmark testing of a diffusive and an inertial formulation of the de St. Venant equations implemented within the LISFLOOD-FP hydraulic model using high resolution terrestrial LiDAR data. The models are applied to a hypothetical flooding scenario in a section of Alcester, UK which experienced significant surface water flooding in the June and July floods of 2007 in the UK. The sensitivity of water elevation and velocity simulations to model formulation and grid resolution are analyzed. The differences in depth and velocity estimates between the diffusive and inertial approximations are within 10% of the simulated value but inertial effects persist at the wetting front in steep catchments. Both models portray a similar scale dependency between 50 cm and 5 m resolution which reiterates previous findings that errors in coarse scale topographic data sets are significantly larger than differences between numerical approximations. In particular, these results confirm the need to distinctly represent the camber and curbs of roads in the numerical grid when simulating surface water flooding events. Furthermore, although water depth estimates at grid scales coarser than 1 m appear robust, velocity estimates at these scales seem to be inconsistent compared to the 50 cm benchmark. The inertial formulation is shown to reduce computational cost by up to three orders of magnitude at high resolutions thus making simulations at this scale viable in practice compared to diffusive models. For the first time, this paper highlights the utility of high resolution terrestrial LiDAR data to inform small-scale flood risk management studies.

PHISICS/RELAP5-3D RESULTS FOR EXERCISES II-1 AND II-2 OF THE OECD/NEA MHTGR-350 BENCHMARK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strydom, Gerhard

2016-03-01

The Idaho National Laboratory (INL) Advanced Reactor Technologies (ART) High-Temperature Gas-Cooled Reactor (HTGR) Methods group currently leads the Modular High-Temperature Gas-Cooled Reactor (MHTGR) 350 benchmark. The benchmark consists of a set of lattice-depletion, steady-state, and transient problems that can be used by HTGR simulation groups to assess the performance of their code suites. The paper summarizes the results obtained for the first two transient exercises defined for Phase II of the benchmark. The Parallel and Highly Innovative Simulation for INL Code System (PHISICS), coupled with the INL system code RELAP5-3D, was used to generate the results for the Depressurized Conductionmore » Cooldown (DCC) (exercise II-1a) and Pressurized Conduction Cooldown (PCC) (exercise II-2) transients. These exercises require the time-dependent simulation of coupled neutronics and thermal-hydraulics phenomena, and utilize the steady-state solution previously obtained for exercise I-3 of Phase I. This paper also includes a comparison of the benchmark results obtained with a traditional system code “ring” model against a more detailed “block” model that include kinetics feedback on an individual block level and thermal feedbacks on a triangular sub-mesh. The higher spatial fidelity that can be obtained by the block model is illustrated with comparisons of the maximum fuel temperatures, especially in the case of natural convection conditions that dominate the DCC and PCC events. Differences up to 125 K (or 10%) were observed between the ring and block model predictions of the DCC transient, mostly due to the block model’s capability of tracking individual block decay powers and more detailed helium flow distributions. In general, the block model only required DCC and PCC calculation times twice as long as the ring models, and it therefore seems that the additional development and calculation time required for the block model could be worth the gain that can be obtained in the spatial resolution« less

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Peiyuan; Brown, Timothy; Fullmer, William D.

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling ofmore » the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.« less

Determining the sample size required to establish whether a medical device is non-inferior to an external benchmark.

PubMed

Sayers, Adrian; Crowther, Michael J; Judge, Andrew; Whitehouse, Michael R; Blom, Ashley W

2017-08-28

The use of benchmarks to assess the performance of implants such as those used in arthroplasty surgery is a widespread practice. It provides surgeons, patients and regulatory authorities with the reassurance that implants used are safe and effective. However, it is not currently clear how or how many implants should be statistically compared with a benchmark to assess whether or not that implant is superior, equivalent, non-inferior or inferior to the performance benchmark of interest.We aim to describe the methods and sample size required to conduct a one-sample non-inferiority study of a medical device for the purposes of benchmarking. Simulation study. Simulation study of a national register of medical devices. We simulated data, with and without a non-informative competing risk, to represent an arthroplasty population and describe three methods of analysis (z-test, 1-Kaplan-Meier and competing risks) commonly used in surgical research. We evaluate the performance of each method using power, bias, root-mean-square error, coverage and CI width. 1-Kaplan-Meier provides an unbiased estimate of implant net failure, which can be used to assess if a surgical device is non-inferior to an external benchmark. Small non-inferiority margins require significantly more individuals to be at risk compared with current benchmarking standards. A non-inferiority testing paradigm provides a useful framework for determining if an implant meets the required performance defined by an external benchmark. Current contemporary benchmarking standards have limited power to detect non-inferiority, and substantially larger samples sizes, in excess of 3200 procedures, are required to achieve a power greater than 60%. It is clear when benchmarking implant performance, net failure estimated using 1-KM is preferential to crude failure estimated by competing risk models. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Numerical modeling of fluid and electrical currents through geometries based on synchrotron X-ray tomographic images of reservoir rocks using Avizo and COMSOL

NASA Astrophysics Data System (ADS)

Bird, M. B.; Butler, S. L.; Hawkes, C. D.; Kotzer, T.

2014-12-01

The use of numerical simulations to model physical processes occurring within subvolumes of rock samples that have been characterized using advanced 3D imaging techniques is becoming increasingly common. Not only do these simulations allow for the determination of macroscopic properties like hydraulic permeability and electrical formation factor, but they also allow the user to visualize processes taking place at the pore scale and they allow for multiple different processes to be simulated on the same geometry. Most efforts to date have used specialized research software for the purpose of simulations. In this contribution, we outline the steps taken to use commercial software Avizo to transform a 3D synchrotron X-ray-derived tomographic image of a rock core sample to an STL (STereoLithography) file which can be imported into the commercial multiphysics modeling package COMSOL. We demonstrate that the use of COMSOL to perform fluid and electrical current flow simulations through the pore spaces. The permeability and electrical formation factor of the sample are calculated and compared with laboratory-derived values and benchmark calculations. Although the simulation domains that we were able to model on a desk top computer were significantly smaller than representative elementary volumes, and we were able to establish Kozeny-Carman and Archie's Law trends on which laboratory measurements and previous benchmark solutions fall. The rock core samples include a Fountainebleau sandstone used for benchmarking and a marly dolostone sampled from a well in the Weyburn oil field of southeastern Saskatchewan, Canada. Such carbonates are known to have complicated pore structures compared with sandstones, yet we are able to calculate reasonable macroscopic properties. We discuss the computing resources required.

Design and Application of a Community Land Benchmarking System for Earth System Models

NASA Astrophysics Data System (ADS)

Mu, M.; Hoffman, F. M.; Lawrence, D. M.; Riley, W. J.; Keppel-Aleks, G.; Koven, C. D.; Kluzek, E. B.; Mao, J.; Randerson, J. T.

2015-12-01

Benchmarking has been widely used to assess the ability of climate models to capture the spatial and temporal variability of observations during the historical era. For the carbon cycle and terrestrial ecosystems, the design and development of an open-source community platform has been an important goal as part of the International Land Model Benchmarking (ILAMB) project. Here we developed a new benchmarking software system that enables the user to specify the models, benchmarks, and scoring metrics, so that results can be tailored to specific model intercomparison projects. Evaluation data sets included soil and aboveground carbon stocks, fluxes of energy, carbon and water, burned area, leaf area, and climate forcing and response variables. We used this system to evaluate simulations from the 5th Phase of the Coupled Model Intercomparison Project (CMIP5) with prognostic atmospheric carbon dioxide levels over the period from 1850 to 2005 (i.e., esmHistorical simulations archived on the Earth System Grid Federation). We found that the multi-model ensemble had a high bias in incoming solar radiation across Asia, likely as a consequence of incomplete representation of aerosol effects in this region, and in South America, primarily as a consequence of a low bias in mean annual precipitation. The reduced precipitation in South America had a larger influence on gross primary production than the high bias in incoming light, and as a consequence gross primary production had a low bias relative to the observations. Although model to model variations were large, the multi-model mean had a positive bias in atmospheric carbon dioxide that has been attributed in past work to weak ocean uptake of fossil emissions. In mid latitudes of the northern hemisphere, most models overestimate latent heat fluxes in the early part of the growing season, and underestimate these fluxes in mid-summer and early fall, whereas sensible heat fluxes show the opposite trend.

Engine dynamic analysis with general nonlinear finite element codes. Part 2: Bearing element implementation overall numerical characteristics and benchmaking

NASA Technical Reports Server (NTRS)

Padovan, J.; Adams, M.; Fertis, J.; Zeid, I.; Lam, P.

1982-01-01

Finite element codes are used in modelling rotor-bearing-stator structure common to the turbine industry. Engine dynamic simulation is used by developing strategies which enable the use of available finite element codes. benchmarking the elements developed are benchmarked by incorporation into a general purpose code (ADINA); the numerical characteristics of finite element type rotor-bearing-stator simulations are evaluated through the use of various types of explicit/implicit numerical integration operators. Improving the overall numerical efficiency of the procedure is improved.

Model evaluation using a community benchmarking system for land surface models

NASA Astrophysics Data System (ADS)

Mu, M.; Hoffman, F. M.; Lawrence, D. M.; Riley, W. J.; Keppel-Aleks, G.; Kluzek, E. B.; Koven, C. D.; Randerson, J. T.

2014-12-01

Evaluation of atmosphere, ocean, sea ice, and land surface models is an important step in identifying deficiencies in Earth system models and developing improved estimates of future change. For the land surface and carbon cycle, the design of an open-source system has been an important objective of the International Land Model Benchmarking (ILAMB) project. Here we evaluated CMIP5 and CLM models using a benchmarking system that enables users to specify models, data sets, and scoring systems so that results can be tailored to specific model intercomparison projects. Our scoring system used information from four different aspects of global datasets, including climatological mean spatial patterns, seasonal cycle dynamics, interannual variability, and long-term trends. Variable-to-variable comparisons enable investigation of the mechanistic underpinnings of model behavior, and allow for some control of biases in model drivers. Graphics modules allow users to evaluate model performance at local, regional, and global scales. Use of modular structures makes it relatively easy for users to add new variables, diagnostic metrics, benchmarking datasets, or model simulations. Diagnostic results are automatically organized into HTML files, so users can conveniently share results with colleagues. We used this system to evaluate atmospheric carbon dioxide, burned area, global biomass and soil carbon stocks, net ecosystem exchange, gross primary production, ecosystem respiration, terrestrial water storage, evapotranspiration, and surface radiation from CMIP5 historical and ESM historical simulations. We found that the multi-model mean often performed better than many of the individual models for most variables. We plan to publicly release a stable version of the software during fall of 2014 that has land surface, carbon cycle, hydrology, radiation and energy cycle components.

Results of the 2013 UT modeling benchmark obtained with models implemented in CIVA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toullelan, Gwénaël; Raillon, Raphaële; Chatillon, Sylvain

The 2013 Ultrasonic Testing (UT) modeling benchmark concerns direct echoes from side drilled holes (SDH), flat bottom holes (FBH) and corner echoes from backwall breaking artificial notches inspected with a matrix phased array probe. This communication presents the results obtained with the models implemented in the CIVA software: the pencilmodel is used to compute the field radiated by the probe, the Kirchhoff approximation is applied to predict the response of FBH and notches and the SOV (Separation Of Variables) model is used for the SDH responses. The comparison between simulated and experimental results are presented and discussed.

GLOFRIM v1.0 - A globally applicable computational framework for integrated hydrological-hydrodynamic modelling

NASA Astrophysics Data System (ADS)

Hoch, Jannis M.; Neal, Jeffrey C.; Baart, Fedor; van Beek, Rens; Winsemius, Hessel C.; Bates, Paul D.; Bierkens, Marc F. P.

2017-10-01

We here present GLOFRIM, a globally applicable computational framework for integrated hydrological-hydrodynamic modelling. GLOFRIM facilitates spatially explicit coupling of hydrodynamic and hydrologic models and caters for an ensemble of models to be coupled. It currently encompasses the global hydrological model PCR-GLOBWB as well as the hydrodynamic models Delft3D Flexible Mesh (DFM; solving the full shallow-water equations and allowing for spatially flexible meshing) and LISFLOOD-FP (LFP; solving the local inertia equations and running on regular grids). The main advantages of the framework are its open and free access, its global applicability, its versatility, and its extensibility with other hydrological or hydrodynamic models. Before applying GLOFRIM to an actual test case, we benchmarked both DFM and LFP for a synthetic test case. Results show that for sub-critical flow conditions, discharge response to the same input signal is near-identical for both models, which agrees with previous studies. We subsequently applied the framework to the Amazon River basin to not only test the framework thoroughly, but also to perform a first-ever benchmark of flexible and regular grids on a large-scale. Both DFM and LFP produce comparable results in terms of simulated discharge with LFP exhibiting slightly higher accuracy as expressed by a Kling-Gupta efficiency of 0.82 compared to 0.76 for DFM. However, benchmarking inundation extent between DFM and LFP over the entire study area, a critical success index of 0.46 was obtained, indicating that the models disagree as often as they agree. Differences between models in both simulated discharge and inundation extent are to a large extent attributable to the gridding techniques employed. In fact, the results show that both the numerical scheme of the inundation model and the gridding technique can contribute to deviations in simulated inundation extent as we control for model forcing and boundary conditions. This study shows that the presented computational framework is robust and widely applicable. GLOFRIM is designed as open access and easily extendable, and thus we hope that other large-scale hydrological and hydrodynamic models will be added. Eventually, more locally relevant processes would be captured and more robust model inter-comparison, benchmarking, and ensemble simulations of flood hazard on a large scale would be allowed for.

Benchmarking Model Variants in Development of a Hardware-in-the-Loop Simulation System

NASA Technical Reports Server (NTRS)

Aretskin-Hariton, Eliot D.; Zinnecker, Alicia M.; Kratz, Jonathan L.; Culley, Dennis E.; Thomas, George L.

2016-01-01

Distributed engine control architecture presents a significant increase in complexity over traditional implementations when viewed from the perspective of system simulation and hardware design and test. Even if the overall function of the control scheme remains the same, the hardware implementation can have a significant effect on the overall system performance due to differences in the creation and flow of data between control elements. A Hardware-in-the-Loop (HIL) simulation system is under development at NASA Glenn Research Center that enables the exploration of these hardware dependent issues. The system is based on, but not limited to, the Commercial Modular Aero-Propulsion System Simulation 40k (C-MAPSS40k). This paper describes the step-by-step conversion from the self-contained baseline model to the hardware in the loop model, and the validation of each step. As the control model hardware fidelity was improved during HIL system development, benchmarking simulations were performed to verify that engine system performance characteristics remained the same. The results demonstrate the goal of the effort; the new HIL configurations have similar functionality and performance compared to the baseline C-MAPSS40k system.

ViSAPy: a Python tool for biophysics-based generation of virtual spiking activity for evaluation of spike-sorting algorithms.

PubMed

Hagen, Espen; Ness, Torbjørn V; Khosrowshahi, Amir; Sørensen, Christina; Fyhn, Marianne; Hafting, Torkel; Franke, Felix; Einevoll, Gaute T

2015-04-30

New, silicon-based multielectrodes comprising hundreds or more electrode contacts offer the possibility to record spike trains from thousands of neurons simultaneously. This potential cannot be realized unless accurate, reliable automated methods for spike sorting are developed, in turn requiring benchmarking data sets with known ground-truth spike times. We here present a general simulation tool for computing benchmarking data for evaluation of spike-sorting algorithms entitled ViSAPy (Virtual Spiking Activity in Python). The tool is based on a well-established biophysical forward-modeling scheme and is implemented as a Python package built on top of the neuronal simulator NEURON and the Python tool LFPy. ViSAPy allows for arbitrary combinations of multicompartmental neuron models and geometries of recording multielectrodes. Three example benchmarking data sets are generated, i.e., tetrode and polytrode data mimicking in vivo cortical recordings and microelectrode array (MEA) recordings of in vitro activity in salamander retinas. The synthesized example benchmarking data mimics salient features of typical experimental recordings, for example, spike waveforms depending on interspike interval. ViSAPy goes beyond existing methods as it includes biologically realistic model noise, synaptic activation by recurrent spiking networks, finite-sized electrode contacts, and allows for inhomogeneous electrical conductivities. ViSAPy is optimized to allow for generation of long time series of benchmarking data, spanning minutes of biological time, by parallel execution on multi-core computers. ViSAPy is an open-ended tool as it can be generalized to produce benchmarking data or arbitrary recording-electrode geometries and with various levels of complexity. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Using SPARK as a Solver for Modelica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wetter, Michael; Wetter, Michael; Haves, Philip

Modelica is an object-oriented acausal modeling language that is well positioned to become a de-facto standard for expressing models of complex physical systems. To simulate a model expressed in Modelica, it needs to be translated into executable code. For generating run-time efficient code, such a translation needs to employ algebraic formula manipulations. As the SPARK solver has been shown to be competitive for generating such code but currently cannot be used with the Modelica language, we report in this paper how SPARK's symbolic and numerical algorithms can be implemented in OpenModelica, an open-source implementation of a Modelica modeling and simulationmore » environment. We also report benchmark results that show that for our air flow network simulation benchmark, the SPARK solver is competitive with Dymola, which is believed to provide the best solver for Modelica.« less

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, D. H.; Barszcz, E.; Barton, J. T.; Carter, R. L.; Lasinski, T. A.; Browning, D. S.; Dagum, L.; Fatoohi, R. A.; Frederickson, P. O.; Schreiber, R. S.

1991-01-01

A new set of benchmarks has been developed for the performance evaluation of highly parallel supercomputers in the framework of the NASA Ames Numerical Aerodynamic Simulation (NAS) Program. These consist of five 'parallel kernel' benchmarks and three 'simulated application' benchmarks. Together they mimic the computation and data movement characteristics of large-scale computational fluid dynamics applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification-all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Ye; Ma, Xiaosong; Liu, Qing Gary

2015-01-01

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters tomore » create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.« less

Evaluation of the synoptic and mesoscale predictive capabilities of a mesoscale atmospheric simulation system

NASA Technical Reports Server (NTRS)

Koch, S. E.; Skillman, W. C.; Kocin, P. J.; Wetzel, P. J.; Brill, K.; Keyser, D. A.; Mccumber, M. C.

1983-01-01

The overall performance characteristics of a limited area, hydrostatic, fine (52 km) mesh, primitive equation, numerical weather prediction model are determined in anticipation of satellite data assimilations with the model. The synoptic and mesoscale predictive capabilities of version 2.0 of this model, the Mesoscale Atmospheric Simulation System (MASS 2.0), were evaluated. The two part study is based on a sample of approximately thirty 12h and 24h forecasts of atmospheric flow patterns during spring and early summer. The synoptic scale evaluation results benchmark the performance of MASS 2.0 against that of an operational, synoptic scale weather prediction model, the Limited area Fine Mesh (LFM). The large sample allows for the calculation of statistically significant measures of forecast accuracy and the determination of systematic model errors. The synoptic scale benchmark is required before unsmoothed mesoscale forecast fields can be seriously considered.

Generalizable open source urban water portfolio simulation framework demonstrated using a multi-objective risk-based planning benchmark problem.

NASA Astrophysics Data System (ADS)

Trindade, B. C.; Reed, P. M.

2017-12-01

The growing access and reduced cost for computing power in recent years has promoted rapid development and application of multi-objective water supply portfolio planning. As this trend continues there is a pressing need for flexible risk-based simulation frameworks and improved algorithm benchmarking for emerging classes of water supply planning and management problems. This work contributes the Water Utilities Management and Planning (WUMP) model: a generalizable and open source simulation framework designed to capture how water utilities can minimize operational and financial risks by regionally coordinating planning and management choices, i.e. making more efficient and coordinated use of restrictions, water transfers and financial hedging combined with possible construction of new infrastructure. We introduce the WUMP simulation framework as part of a new multi-objective benchmark problem for planning and management of regionally integrated water utility companies. In this problem, a group of fictitious water utilities seek to balance the use of the mentioned reliability driven actions (e.g., restrictions, water transfers and infrastructure pathways) and their inherent financial risks. Several traits of this problem make it ideal for a benchmark problem, namely the presence of (1) strong non-linearities and discontinuities in the Pareto front caused by the step-wise nature of the decision making formulation and by the abrupt addition of storage through infrastructure construction, (2) noise due to the stochastic nature of the streamflows and water demands, and (3) non-separability resulting from the cooperative formulation of the problem, in which decisions made by stakeholder may substantially impact others. Both the open source WUMP simulation framework and its demonstration in a challenging benchmarking example hold value for promoting broader advances in urban water supply portfolio planning for regions confronting change.

Design and development of a community carbon cycle benchmarking system for CMIP5 models

NASA Astrophysics Data System (ADS)

Mu, M.; Hoffman, F. M.; Lawrence, D. M.; Riley, W. J.; Keppel-Aleks, G.; Randerson, J. T.

2013-12-01

Benchmarking has been widely used to assess the ability of atmosphere, ocean, sea ice, and land surface models to capture the spatial and temporal variability of observations during the historical period. For the carbon cycle and terrestrial ecosystems, the design and development of an open-source community platform has been an important goal as part of the International Land Model Benchmarking (ILAMB) project. Here we designed and developed a software system that enables the user to specify the models, benchmarks, and scoring systems so that results can be tailored to specific model intercomparison projects. We used this system to evaluate the performance of CMIP5 Earth system models (ESMs). Our scoring system used information from four different aspects of climate, including the climatological mean spatial pattern of gridded surface variables, seasonal cycle dynamics, the amplitude of interannual variability, and long-term decadal trends. We used this system to evaluate burned area, global biomass stocks, net ecosystem exchange, gross primary production, and ecosystem respiration from CMIP5 historical simulations. Initial results indicated that the multi-model mean often performed better than many of the individual models for most of the observational constraints.

High-order continuum kinetic method for modeling plasma dynamics in phase space

DOE PAGES

Vogman, G. V.; Colella, P.; Shumlak, U.

2014-12-15

Continuum methods offer a high-fidelity means of simulating plasma kinetics. While computationally intensive, these methods are advantageous because they can be cast in conservation-law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Advances in continuum method capabilities for modeling kinetic phenomena in plasmas require the development of validation tools in higher dimensional phase space and an ability to handle non-cartesian geometries. To that end, a new benchmark for validating Vlasov-Poisson simulations in 3D (x,v x,v y) is presented. The benchmark is based on the Dory-Guest-Harris instability and is successfully used to validate a continuummore » finite volume algorithm. To address challenges associated with non-cartesian geometries, unique features of cylindrical phase space coordinates are described. Preliminary results of continuum kinetic simulations in 4D (r,z,v r,v z) phase space are presented.« less

Increasing the relevance of GCM simulations for Climate Services

NASA Astrophysics Data System (ADS)

Smith, L. A.; Suckling, E.

2012-12-01

The design and interpretation of model simulations for climate services differ significantly from experimental design for the advancement of the fundamental research on predictability that underpins it. Climate services consider the sources of best information available today; this calls for a frank evaluation of model skill in the face of statistical benchmarks defined by empirical models. The fact that Physical simulation models are thought to provide the only reliable method for extrapolating into conditions not previously observed has no bearing on whether or not today's simulation models outperform empirical models. Evidence on the length scales on which today's simulation models fail to outperform empirical benchmarks is presented; it is illustrated that this occurs even on global scales in decadal prediction. At all timescales considered thus far (as of July 2012), predictions based on simulation models are improved by blending with the output of statistical models. Blending is shown to be more interesting in the climate context than it is in the weather context, where blending with a history-based climatology is straightforward. As GCMs improve and as the Earth's climate moves further from that of the last century, the skill from simulation models and their relevance to climate services is expected to increase. Examples from both seasonal and decadal forecasting will be used to discuss a third approach that may increase the role of current GCMs more quickly. Specifically, aspects of the experimental design in previous hind cast experiments are shown to hinder the use of GCM simulations for climate services. Alternative designs are proposed. The value in revisiting Thompson's classic approach to improving weather forecasting in the fifties in the context of climate services is discussed.

Evaluation of control strategies using an oxidation ditch benchmark.

PubMed

Abusam, A; Keesman, K J; Spanjers, H; van, Straten G; Meinema, K

2002-01-01

This paper presents validation and implementation results of a benchmark developed for a specific full-scale oxidation ditch wastewater treatment plant. A benchmark is a standard simulation procedure that can be used as a tool in evaluating various control strategies proposed for wastewater treatment plants. It is based on model and performance criteria development. Testing of this benchmark, by comparing benchmark predictions to real measurements of the electrical energy consumptions and amounts of disposed sludge for a specific oxidation ditch WWTP, has shown that it can (reasonably) be used for evaluating the performance of this WWTP. Subsequently, the validated benchmark was then used in evaluating some basic and advanced control strategies. Some of the interesting results obtained are the following: (i) influent flow splitting ratio, between the first and the fourth aerated compartments of the ditch, has no significant effect on the TN concentrations in the effluent, and (ii) for evaluation of long-term control strategies, future benchmarks need to be able to assess settlers' performance.

Benchmark of the local drift-kinetic models for neoclassical transport simulation in helical plasmas

NASA Astrophysics Data System (ADS)

Huang, B.; Satake, S.; Kanno, R.; Sugama, H.; Matsuoka, S.

2017-02-01

The benchmarks of the neoclassical transport codes based on the several local drift-kinetic models are reported here. Here, the drift-kinetic models are zero orbit width (ZOW), zero magnetic drift, DKES-like, and global, as classified in Matsuoka et al. [Phys. Plasmas 22, 072511 (2015)]. The magnetic geometries of Helically Symmetric Experiment, Large Helical Device (LHD), and Wendelstein 7-X are employed in the benchmarks. It is found that the assumption of E ×B incompressibility causes discrepancy of neoclassical radial flux and parallel flow among the models when E ×B is sufficiently large compared to the magnetic drift velocities. For example, Mp≤0.4 where Mp is the poloidal Mach number. On the other hand, when E ×B and the magnetic drift velocities are comparable, the tangential magnetic drift, which is included in both the global and ZOW models, fills the role of suppressing unphysical peaking of neoclassical radial-fluxes found in the other local models at Er≃0 . In low collisionality plasmas, in particular, the tangential drift effect works well to suppress such unphysical behavior of the radial transport caused in the simulations. It is demonstrated that the ZOW model has the advantage of mitigating the unphysical behavior in the several magnetic geometries, and that it also implements the evaluation of bootstrap current in LHD with the low computation cost compared to the global model.

Large eddy simulation of the FDA benchmark nozzle for a Reynolds number of 6500.

PubMed

Janiga, Gábor

2014-04-01

This work investigates the flow in a benchmark nozzle model of an idealized medical device proposed by the FDA using computational fluid dynamics (CFD). It was in particular shown that a proper modeling of the transitional flow features is particularly challenging, leading to large discrepancies and inaccurate predictions from the different research groups using Reynolds-averaged Navier-Stokes (RANS) modeling. In spite of the relatively simple, axisymmetric computational geometry, the resulting turbulent flow is fairly complex and non-axisymmetric, in particular due to the sudden expansion. The resulting flow cannot be well predicted with simple modeling approaches. Due to the varying diameters and flow velocities encountered in the nozzle, different typical flow regions and regimes can be distinguished, from laminar to transitional and to weakly turbulent. The purpose of the present work is to re-examine the FDA-CFD benchmark nozzle model at a Reynolds number of 6500 using large eddy simulation (LES). The LES results are compared with published experimental data obtained by Particle Image Velocimetry (PIV) and an excellent agreement can be observed considering the temporally averaged flow velocities. Different flow regimes are characterized by computing the temporal energy spectra at different locations along the main axis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Benchmarking electrophysiological models of human atrial myocytes

PubMed Central

Wilhelms, Mathias; Hettmann, Hanne; Maleckar, Mary M.; Koivumäki, Jussi T.; Dössel, Olaf; Seemann, Gunnar

2013-01-01

Mathematical modeling of cardiac electrophysiology is an insightful method to investigate the underlying mechanisms responsible for arrhythmias such as atrial fibrillation (AF). In past years, five models of human atrial electrophysiology with different formulations of ionic currents, and consequently diverging properties, have been published. The aim of this work is to give an overview of strengths and weaknesses of these models depending on the purpose and the general requirements of simulations. Therefore, these models were systematically benchmarked with respect to general mathematical properties and their ability to reproduce certain electrophysiological phenomena, such as action potential (AP) alternans. To assess the models' ability to replicate modified properties of human myocytes and tissue in cardiac disease, electrical remodeling in chronic atrial fibrillation (cAF) was chosen as test case. The healthy and remodeled model variants were compared with experimental results in single-cell, 1D and 2D tissue simulations to investigate AP and restitution properties, as well as the initiation of reentrant circuits. PMID:23316167

A benchmark for fault tolerant flight control evaluation

NASA Astrophysics Data System (ADS)

Smaili, H.; Breeman, J.; Lombaerts, T.; Stroosma, O.

2013-12-01

A large transport aircraft simulation benchmark (REconfigurable COntrol for Vehicle Emergency Return - RECOVER) has been developed within the GARTEUR (Group for Aeronautical Research and Technology in Europe) Flight Mechanics Action Group 16 (FM-AG(16)) on Fault Tolerant Control (2004 2008) for the integrated evaluation of fault detection and identification (FDI) and reconfigurable flight control strategies. The benchmark includes a suitable set of assessment criteria and failure cases, based on reconstructed accident scenarios, to assess the potential of new adaptive control strategies to improve aircraft survivability. The application of reconstruction and modeling techniques, based on accident flight data, has resulted in high-fidelity nonlinear aircraft and fault models to evaluate new Fault Tolerant Flight Control (FTFC) concepts and their real-time performance to accommodate in-flight failures.

An international land-biosphere model benchmarking activity for the IPCC Fifth Assessment Report (AR5)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffman, Forrest M; Randerson, James T; Thornton, Peter E

2009-12-01

The need to capture important climate feedbacks in general circulation models (GCMs) has resulted in efforts to include atmospheric chemistry and land and ocean biogeochemistry into the next generation of production climate models, called Earth System Models (ESMs). While many terrestrial and ocean carbon models have been coupled to GCMs, recent work has shown that such models can yield a wide range of results (Friedlingstein et al., 2006). This work suggests that a more rigorous set of global offline and partially coupled experiments, along with detailed analyses of processes and comparisons with measurements, are needed. The Carbon-Land Model Intercomparison Projectmore » (C-LAMP) was designed to meet this need by providing a simulation protocol and model performance metrics based upon comparisons against best-available satellite- and ground-based measurements (Hoffman et al., 2007). Recently, a similar effort in Europe, called the International Land Model Benchmark (ILAMB) Project, was begun to assess the performance of European land surface models. These two projects will now serve as prototypes for a proposed international land-biosphere model benchmarking activity for those models participating in the IPCC Fifth Assessment Report (AR5). Initially used for model validation for terrestrial biogeochemistry models in the NCAR Community Land Model (CLM), C-LAMP incorporates a simulation protocol for both offline and partially coupled simulations using a prescribed historical trajectory of atmospheric CO2 concentrations. Models are confronted with data through comparisons against AmeriFlux site measurements, MODIS satellite observations, NOAA Globalview flask records, TRANSCOM inversions, and Free Air CO2 Enrichment (FACE) site measurements. Both sets of experiments have been performed using two different terrestrial biogeochemistry modules coupled to the CLM version 3 in the Community Climate System Model version 3 (CCSM3): the CASA model of Fung, et al., and the carbon-nitrogen (CN) model of Thornton. Comparisons of the CLM3 offline results against observational datasets have been performed and are described in Randerson et al. (2009). CLM version 4 has been evaluated using C-LAMP, showing improvement in many of the metrics. Efforts are now underway to initiate a Nitrogen-Land Model Intercomparison Project (N-LAMP) to better constrain the effects of the nitrogen cycle in biosphere models. Presented will be new results from C-LAMP for CLM4, initial N-LAMP developments, and the proposed land-biosphere model benchmarking activity.« less

Modeling of turbulent separated flows for aerodynamic applications

NASA Technical Reports Server (NTRS)

Marvin, J. G.

1983-01-01

Steady, high speed, compressible separated flows modeled through numerical simulations resulting from solutions of the mass-averaged Navier-Stokes equations are reviewed. Emphasis is placed on benchmark flows that represent simplified (but realistic) aerodynamic phenomena. These include impinging shock waves, compression corners, glancing shock waves, trailing edge regions, and supersonic high angle of attack flows. A critical assessment of modeling capabilities is provided by comparing the numerical simulations with experiment. The importance of combining experiment, numerical algorithm, grid, and turbulence model to effectively develop this potentially powerful simulation technique is stressed.

Simulation of guided-wave ultrasound propagation in composite laminates: Benchmark comparisons of numerical codes and experiment.

PubMed

Leckey, Cara A C; Wheeler, Kevin R; Hafiychuk, Vasyl N; Hafiychuk, Halyna; Timuçin, Doğan A

2018-03-01

Ultrasonic wave methods constitute the leading physical mechanism for nondestructive evaluation (NDE) and structural health monitoring (SHM) of solid composite materials, such as carbon fiber reinforced polymer (CFRP) laminates. Computational models of ultrasonic wave excitation, propagation, and scattering in CFRP composites can be extremely valuable in designing practicable NDE and SHM hardware, software, and methodologies that accomplish the desired accuracy, reliability, efficiency, and coverage. The development and application of ultrasonic simulation approaches for composite materials is an active area of research in the field of NDE. This paper presents comparisons of guided wave simulations for CFRP composites implemented using four different simulation codes: the commercial finite element modeling (FEM) packages ABAQUS, ANSYS, and COMSOL, and a custom code executing the Elastodynamic Finite Integration Technique (EFIT). Benchmark comparisons are made between the simulation tools and both experimental laser Doppler vibrometry data and theoretical dispersion curves. A pristine and a delamination type case (Teflon insert in the experimental specimen) is studied. A summary is given of the accuracy of simulation results and the respective computational performance of the four different simulation tools. Published by Elsevier B.V.

Groundwater flow with energy transport and water-ice phase change: Numerical simulations, benchmarks, and application to freezing in peat bogs

USGS Publications Warehouse

McKenzie, J.M.; Voss, C.I.; Siegel, D.I.

2007-01-01

In northern peatlands, subsurface ice formation is an important process that can control heat transport, groundwater flow, and biological activity. Temperature was measured over one and a half years in a vertical profile in the Red Lake Bog, Minnesota. To successfully simulate the transport of heat within the peat profile, the U.S. Geological Survey's SUTRA computer code was modified. The modified code simulates fully saturated, coupled porewater-energy transport, with freezing and melting porewater, and includes proportional heat capacity and thermal conductivity of water and ice, decreasing matrix permeability due to ice formation, and latent heat. The model is verified by correctly simulating the Lunardini analytical solution for ice formation in a porous medium with a mixed ice-water zone. The modified SUTRA model correctly simulates the temperature and ice distributions in the peat bog. Two possible benchmark problems for groundwater and energy transport with ice formation and melting are proposed that may be used by other researchers for code comparison. ?? 2006 Elsevier Ltd. All rights reserved.

Issues in benchmarking human reliability analysis methods : a literature review.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lois, Erasmia; Forester, John Alan; Tran, Tuan Q.

There is a diversity of human reliability analysis (HRA) methods available for use in assessing human performance within probabilistic risk assessment (PRA). Due to the significant differences in the methods, including the scope, approach, and underlying models, there is a need for an empirical comparison investigating the validity and reliability of the methods. To accomplish this empirical comparison, a benchmarking study is currently underway that compares HRA methods with each other and against operator performance in simulator studies. In order to account for as many effects as possible in the construction of this benchmarking study, a literature review was conducted,more » reviewing past benchmarking studies in the areas of psychology and risk assessment. A number of lessons learned through these studies are presented in order to aid in the design of future HRA benchmarking endeavors.« less

Issues in Benchmarking Human Reliability Analysis Methods: A Literature Review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronald L. Boring; Stacey M. L. Hendrickson; John A. Forester

There is a diversity of human reliability analysis (HRA) methods available for use in assessing human performance within probabilistic risk assessments (PRA). Due to the significant differences in the methods, including the scope, approach, and underlying models, there is a need for an empirical comparison investigating the validity and reliability of the methods. To accomplish this empirical comparison, a benchmarking study comparing and evaluating HRA methods in assessing operator performance in simulator experiments is currently underway. In order to account for as many effects as possible in the construction of this benchmarking study, a literature review was conducted, reviewing pastmore » benchmarking studies in the areas of psychology and risk assessment. A number of lessons learned through these studies are presented in order to aid in the design of future HRA benchmarking endeavors.« less

Using GTO-Velo to Facilitate Communication and Sharing of Simulation Results in Support of the Geothermal Technologies Office Code Comparison Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Signe K.; Purohit, Sumit; Boyd, Lauren W.

The Geothermal Technologies Office Code Comparison Study (GTO-CCS) aims to support the DOE Geothermal Technologies Office in organizing and executing a model comparison activity. This project is directed at testing, diagnosing differences, and demonstrating modeling capabilities of a worldwide collection of numerical simulators for evaluating geothermal technologies. Teams of researchers are collaborating in this code comparison effort, and it is important to be able to share results in a forum where technical discussions can easily take place without requiring teams to travel to a common location. Pacific Northwest National Laboratory has developed an open-source, flexible framework called Velo that providesmore » a knowledge management infrastructure and tools to support modeling and simulation for a variety of types of projects in a number of scientific domains. GTO-Velo is a customized version of the Velo Framework that is being used as the collaborative tool in support of the GTO-CCS project. Velo is designed around a novel integration of a collaborative Web-based environment and a scalable enterprise Content Management System (CMS). The underlying framework provides a flexible and unstructured data storage system that allows for easy upload of files that can be in any format. Data files are organized in hierarchical folders and each folder and each file has a corresponding wiki page for metadata. The user interacts with Velo through a web browser based wiki technology, providing the benefit of familiarity and ease of use. High-level folders have been defined in GTO-Velo for the benchmark problem descriptions, descriptions of simulator/code capabilities, a project notebook, and folders for participating teams. Each team has a subfolder with write access limited only to the team members, where they can upload their simulation results. The GTO-CCS participants are charged with defining the benchmark problems for the study, and as each GTO-CCS Benchmark problem is defined, the problem creator can provide a description using a template on the metadata page corresponding to the benchmark problem folder. Project documents, references and videos of the weekly online meetings are shared via GTO-Velo. A results comparison tool allows users to plot their uploaded simulation results on the fly, along with those of other teams, to facilitate weekly discussions of the benchmark problem results being generated by the teams. GTO-Velo is an invaluable tool providing the project coordinators and team members with a framework for collaboration among geographically dispersed organizations.« less

Mathematical model and metaheuristics for simultaneous balancing and sequencing of a robotic mixed-model assembly line

NASA Astrophysics Data System (ADS)

Li, Zixiang; Janardhanan, Mukund Nilakantan; Tang, Qiuhua; Nielsen, Peter

2018-05-01

This article presents the first method to simultaneously balance and sequence robotic mixed-model assembly lines (RMALB/S), which involves three sub-problems: task assignment, model sequencing and robot allocation. A new mixed-integer programming model is developed to minimize makespan and, using CPLEX solver, small-size problems are solved for optimality. Two metaheuristics, the restarted simulated annealing algorithm and co-evolutionary algorithm, are developed and improved to address this NP-hard problem. The restarted simulated annealing method replaces the current temperature with a new temperature to restart the search process. The co-evolutionary method uses a restart mechanism to generate a new population by modifying several vectors simultaneously. The proposed algorithms are tested on a set of benchmark problems and compared with five other high-performing metaheuristics. The proposed algorithms outperform their original editions and the benchmarked methods. The proposed algorithms are able to solve the balancing and sequencing problem of a robotic mixed-model assembly line effectively and efficiently.

A Monte-Carlo Benchmark of TRIPOLI-4® and MCNP on ITER neutronics

NASA Astrophysics Data System (ADS)

Blanchet, David; Pénéliau, Yannick; Eschbach, Romain; Fontaine, Bruno; Cantone, Bruno; Ferlet, Marc; Gauthier, Eric; Guillon, Christophe; Letellier, Laurent; Proust, Maxime; Mota, Fernando; Palermo, Iole; Rios, Luis; Guern, Frédéric Le; Kocan, Martin; Reichle, Roger

2017-09-01

Radiation protection and shielding studies are often based on the extensive use of 3D Monte-Carlo neutron and photon transport simulations. ITER organization hence recommends the use of MCNP-5 code (version 1.60), in association with the FENDL-2.1 neutron cross section data library, specifically dedicated to fusion applications. The MCNP reference model of the ITER tokamak, the `C-lite', is being continuously developed and improved. This article proposes to develop an alternative model, equivalent to the 'C-lite', but for the Monte-Carlo code TRIPOLI-4®. A benchmark study is defined to test this new model. Since one of the most critical areas for ITER neutronics analysis concerns the assessment of radiation levels and Shutdown Dose Rates (SDDR) behind the Equatorial Port Plugs (EPP), the benchmark is conducted to compare the neutron flux through the EPP. This problem is quite challenging with regard to the complex geometry and considering the important neutron flux attenuation ranging from 1014 down to 108 n•cm-2•s-1. Such code-to-code comparison provides independent validation of the Monte-Carlo simulations, improving the confidence in neutronic results.

Assessing Ecosystem Model Performance in Semiarid Systems

NASA Astrophysics Data System (ADS)

Thomas, A.; Dietze, M.; Scott, R. L.; Biederman, J. A.

2017-12-01

In ecosystem process modelling, comparing outputs to benchmark datasets observed in the field is an important way to validate models, allowing the modelling community to track model performance over time and compare models at specific sites. Multi-model comparison projects as well as models themselves have largely been focused on temperate forests and similar biomes. Semiarid regions, on the other hand, are underrepresented in land surface and ecosystem modelling efforts, and yet will be disproportionately impacted by disturbances such as climate change due to their sensitivity to changes in the water balance. Benchmarking models at semiarid sites is an important step in assessing and improving models' suitability for predicting the impact of disturbance on semiarid ecosystems. In this study, several ecosystem models were compared at a semiarid grassland in southwestern Arizona using PEcAn, or the Predictive Ecosystem Analyzer, an open-source eco-informatics toolbox ideal for creating the repeatable model workflows necessary for benchmarking. Models included SIPNET, DALEC, JULES, ED2, GDAY, LPJ-GUESS, MAESPA, CLM, CABLE, and FATES. Comparison between model output and benchmarks such as net ecosystem exchange (NEE) tended to produce high root mean square error and low correlation coefficients, reflecting poor simulation of seasonality and the tendency for models to create much higher carbon sources than observed. These results indicate that ecosystem models do not currently adequately represent semiarid ecosystem processes.

Numerical simulation of air distribution in a room with a sidewall jet under benchmark test conditions

NASA Astrophysics Data System (ADS)

Zasimova, Marina; Ivanov, Nikolay

2018-05-01

The goal of the study is to validate Large Eddy Simulation (LES) data on mixing ventilation in an isothermal room at conditions of benchmark experiments by Hurnik et al. (2015). The focus is on the accuracy of the mean and rms velocity fields prediction in the quasi-free jet zone of the room with 3D jet supplied from a sidewall rectangular diffuser. Calculations were carried out using the ANSYS Fluent 16.2 software with an algebraic wall-modeled LES subgrid-scale model. CFD results on the mean velocity vector are compared with the Laser Doppler Anemometry data. The difference between the mean velocity vector and the mean air speed in the jet zone, both LES-computed, is presented and discussed.

"Aid to Thought"--Just Simulate It!

ERIC Educational Resources Information Center

Kinczkowski, Linda; Cardon, Phillip; Speelman, Pamela

2015-01-01

This paper provides examples of Aid-to-Thought uses in urban decision making, classroom laboratory planning, and in a ship antiaircraft defense system. Aid-to-Thought modeling and simulations are tools students can use effectively in a STEM classroom while meeting Standards for Technological Literacy Benchmarks O and R. These projects prepare…

Validation of numerical codes for impact and explosion cratering: Impacts on strengthless and metal targets

NASA Astrophysics Data System (ADS)

Pierazzo, E.; Artemieva, N.; Asphaug, E.; Baldwin, E. C.; Cazamias, J.; Coker, R.; Collins, G. S.; Crawford, D. A.; Davison, T.; Elbeshausen, D.; Holsapple, K. A.; Housen, K. R.; Korycansky, D. G.; Wünnemann, K.

2008-12-01

Over the last few decades, rapid improvement of computer capabilities has allowed impact cratering to be modeled with increasing complexity and realism, and has paved the way for a new era of numerical modeling of the impact process, including full, three-dimensional (3D) simulations. When properly benchmarked and validated against observation, computer models offer a powerful tool for understanding the mechanics of impact crater formation. This work presents results from the first phase of a project to benchmark and validate shock codes. A variety of 2D and 3D codes were used in this study, from commercial products like AUTODYN, to codes developed within the scientific community like SOVA, SPH, ZEUS-MP, iSALE, and codes developed at U.S. National Laboratories like CTH, SAGE/RAGE, and ALE3D. Benchmark calculations of shock wave propagation in aluminum-on-aluminum impacts were performed to examine the agreement between codes for simple idealized problems. The benchmark simulations show that variability in code results is to be expected due to differences in the underlying solution algorithm of each code, artificial stability parameters, spatial and temporal resolution, and material models. Overall, the inter-code variability in peak shock pressure as a function of distance is around 10 to 20%. In general, if the impactor is resolved by at least 20 cells across its radius, the underestimation of peak shock pressure due to spatial resolution is less than 10%. In addition to the benchmark tests, three validation tests were performed to examine the ability of the codes to reproduce the time evolution of crater radius and depth observed in vertical laboratory impacts in water and two well-characterized aluminum alloys. Results from these calculations are in good agreement with experiments. There appears to be a general tendency of shock physics codes to underestimate the radius of the forming crater. Overall, the discrepancy between the model and experiment results is between 10 and 20%, similar to the inter-code variability.

The PAC-MAN model: Benchmark case for linear acoustics in computational physics

NASA Astrophysics Data System (ADS)

Ziegelwanger, Harald; Reiter, Paul

2017-10-01

Benchmark cases in the field of computational physics, on the one hand, have to contain a certain complexity to test numerical edge cases and, on the other hand, require the existence of an analytical solution, because an analytical solution allows the exact quantification of the accuracy of a numerical simulation method. This dilemma causes a need for analytical sound field formulations of complex acoustic problems. A well known example for such a benchmark case for harmonic linear acoustics is the ;Cat's Eye model;, which describes the three-dimensional sound field radiated from a sphere with a missing octant analytically. In this paper, a benchmark case for two-dimensional (2D) harmonic linear acoustic problems, viz., the ;PAC-MAN model;, is proposed. The PAC-MAN model describes the radiated and scattered sound field around an infinitely long cylinder with a cut out sector of variable angular width. While the analytical calculation of the 2D sound field allows different angular cut-out widths and arbitrarily positioned line sources, the computational cost associated with the solution of this problem is similar to a 1D problem because of a modal formulation of the sound field in the PAC-MAN model.

Modeling and Simulation With Operational Databases to Enable Dynamic Situation Assessment & Prediction

DTIC Science & Technology

2010-11-01

subsections discuss the design of the simulations. 3.12.1 Lanchester5D Simulation A Lanchester simulation was developed to conduct performance...benchmarks using the WarpIV Kernel and HyperWarpSpeed. The Lanchester simulation contains a user-definable number of grid cells in which blue and red...forces engage in battle using Lanchester equations. Having a user-definable number of grid cells enables the simulation to be stressed with high entity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Nicholas R.; Carlsen, Brett W.; Dixon, Brent W.

Dynamic fuel cycle simulation tools are intended to model holistic transient nuclear fuel cycle scenarios. As with all simulation tools, fuel cycle simulators require verification through unit tests, benchmark cases, and integral tests. Model validation is a vital aspect as well. Although compara-tive studies have been performed, there is no comprehensive unit test and benchmark library for fuel cycle simulator tools. The objective of this paper is to identify the must test functionalities of a fuel cycle simulator tool within the context of specific problems of interest to the Fuel Cycle Options Campaign within the U.S. Department of Energy smore » Office of Nuclear Energy. The approach in this paper identifies the features needed to cover the range of promising fuel cycle options identified in the DOE-NE Fuel Cycle Evaluation and Screening (E&S) and categorizes these features to facilitate prioritization. Features were categorized as essential functions, integrating features, and exemplary capabilities. One objective of this paper is to propose a library of unit tests applicable to each of the essential functions. Another underlying motivation for this paper is to encourage an international dialog on the functionalities and standard test methods for fuel cycle simulator tools.« less

A simple numerical model for membrane oxygenation of an artificial lung machine

NASA Astrophysics Data System (ADS)

Subraveti, Sai Nikhil; Sai, P. S. T.; Viswanathan Pillai, Vinod Kumar; Patnaik, B. S. V.

2015-11-01

Optimal design of membrane oxygenators will have far reaching ramification in the development of artificial heart-lung systems. In the present CFD study, we simulate the gas exchange between the venous blood and air that passes through the hollow fiber membranes on a benchmark device. The gas exchange between the tube side fluid and the shell side venous liquid is modeled by solving mass, momentum conservation equations. The fiber bundle was modelled as a porous block with a bundle porosity of 0.6. The resistance offered by the fiber bundle was estimated by the standard Ergun correlation. The present numerical simulations are validated against available benchmark data. The effect of bundle porosity, bundle size, Reynolds number, non-Newtonian constitutive relation, upstream velocity distribution etc. on the pressure drop, oxygen saturation levels etc. are investigated. To emulate the features of gas transfer past the alveoli, the effect of pulsatility on the membrane oxygenation is also investigated.

Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem.

PubMed

Jansson, Johan; Degirmenci, Niyazi Cem; Hoffman, Johan

2017-09-01

In this paper, we address a 3D fluid-structure interaction benchmark problem that represents important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a streamline diffusion-type stabilization of the balance equations for mass and momentum for the entire continuum in the domain, which is implemented in the Unicorn/FEniCS software framework. A phase marker function and its corresponding transport equation are introduced to select the constitutive law, where the mesh tracks the discontinuous fluid-structure interface. This results in a unified simulation method for fluids and structures. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study. Copyright © 2016 John Wiley & Sons, Ltd.

Can a simple lumped parameter model simulate complex transit time distributions? Benchmarking experiments in a virtual watershed.

NASA Astrophysics Data System (ADS)

Wilusz, D. C.; Maxwell, R. M.; Buda, A. R.; Ball, W. P.; Harman, C. J.

2016-12-01

The catchment transit-time distribution (TTD) is the time-varying, probabilistic distribution of water travel times through a watershed. The TTD is increasingly recognized as a useful descriptor of a catchment's flow and transport processes. However, TTDs are temporally complex and cannot be observed directly at watershed scale. Estimates of TTDs depend on available environmental tracers (such as stable water isotopes) and an assumed model whose parameters can be inverted from tracer data. All tracers have limitations though, such as (typically) short periods of observation or non-conservative behavior. As a result, models that faithfully simulate tracer observations may nonetheless yield TTD estimates with significant errors at certain times and water ages, conditioned on the tracer data available and the model structure. Recent advances have shown that time-varying catchment TTDs can be parsimoniously modeled by the lumped parameter rank StorAge Selection (rSAS) model, in which an rSAS function relates the distribution of water ages in outflows to the composition of age-ranked water in storage. Like other TTD models, rSAS is calibrated and evaluated against environmental tracer data, and the relative influence of tracer-dependent and model-dependent error on its TTD estimates is poorly understood. The purpose of this study is to benchmark the ability of different rSAS formulations to simulate TTDs in a complex, synthetic watershed where the lumped model can be calibrated and directly compared to a virtually "true" TTD. This experimental design allows for isolation of model-dependent error from tracer-dependent error. The integrated hydrologic model ParFlow with SLIM-FAST particle tracking code is used to simulate the watershed and its true TTD. To add field intelligence, the ParFlow model is populated with over forty years of hydrometric and physiographic data from the WE-38 subwatershed of the USDA's Mahantango Creek experimental catchment in PA, USA. The results are intended to give practical insight into tradeoffs between rSAS model structure and skill, and define a new performance benchmark to which other transit time models can be compared.

Computational Investigation of In-Flight Temperature in Shaped Charge Jets and Explosively Formed Penetrators

NASA Astrophysics Data System (ADS)

Sable, Peter; Helminiak, Nathaniel; Harstad, Eric; Gullerud, Arne; Hollenshead, Jeromy; Hertel, Eugene; Sandia National Laboratories Collaboration; Marquette University Collaboration

2017-06-01

With the increasing use of hydrocodes in modeling and system design, experimental benchmarking of software has never been more important. While this has been a large area of focus since the inception of computational design, comparisons with temperature data are sparse due to experimental limitations. A novel temperature measurement technique, magnetic diffusion analysis, has enabled the acquisition of in-flight temperature measurements of hyper velocity projectiles. Using this, an AC-14 bare shaped charge and an LX-14 EFP, both with copper linings, were simulated using CTH to benchmark temperature against experimental results. Particular attention was given to the slug temperature profiles after separation, and the effect of varying equation-of-state and strength models. Simulations are in agreement with experimental, attaining better than 2% error between observed shaped charge temperatures. This varied notably depending on the strength model used. Similar observations were made simulating the EFP case, with a minimum 4% deviation. Jet structures compare well with radiographic images and are consistent with ALEGRA simulations previously conducted. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Quantification of uncertainties for application in detonation simulation

NASA Astrophysics Data System (ADS)

Zheng, Miao; Ma, Zhibo

2016-06-01

Numerical simulation has become an important means in designing detonation systems, and the quantification of its uncertainty is also necessary to reliability certification. As to quantifying the uncertainty, it is the most important to analyze how the uncertainties occur and develop, and how the simulations develop from benchmark models to new models. Based on the practical needs of engineering and the technology of verification & validation, a framework of QU(quantification of uncertainty) is brought forward in the case that simulation is used on detonation system for scientific prediction. An example is offered to describe the general idea of quantification of simulation uncertainties.

Benchmark Problems of the Geothermal Technologies Office Code Comparison Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Mark D.; Podgorney, Robert; Kelkar, Sharad M.

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office has sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulationmore » capabilities to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. Study participants submitted solutions to problems for which their simulation tools were deemed capable or nearly capable. Some participating codes were originally developed for EGS applications whereas some others were designed for different applications but can simulate processes similar to those in EGS. Solution submissions from both were encouraged. In some cases, participants made small incremental changes to their numerical simulation codes to address specific elements of the problem, and in other cases participants submitted solutions with existing simulation tools, acknowledging the limitations of the code. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The problems involved two phases of research, stimulation, development, and circulation in two separate reservoirs. The challenge problems had specific questions to be answered via numerical simulation in three topical areas: 1) reservoir creation/stimulation, 2) reactive and passive transport, and 3) thermal recovery. Whereas the benchmark class of problems were designed to test capabilities for modeling coupled processes under strictly specified conditions, the stated objective for the challenge class of problems was to demonstrate what new understanding of the Fenton Hill experiments could be realized via the application of modern numerical simulation tools by recognized expert practitioners.« less

New Flutter Analysis Technique for Time-Domain Computational Aeroelasticity

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Lung, Shun-Fat

2017-01-01

A new time-domain approach for computing flutter speed is presented. Based on the time-history result of aeroelastic simulation, the unknown unsteady aerodynamics model is estimated using a system identification technique. The full aeroelastic model is generated via coupling the estimated unsteady aerodynamic model with the known linear structure model. The critical dynamic pressure is computed and used in the subsequent simulation until the convergence of the critical dynamic pressure is achieved. The proposed method is applied to a benchmark cantilevered rectangular wing.

MoMaS reactive transport benchmark using PFLOTRAN

NASA Astrophysics Data System (ADS)

Park, H.

2017-12-01

MoMaS benchmark was developed to enhance numerical simulation capability for reactive transport modeling in porous media. The benchmark was published in late September of 2009; it is not taken from a real chemical system, but realistic and numerically challenging tests. PFLOTRAN is a state-of-art massively parallel subsurface flow and reactive transport code that is being used in multiple nuclear waste repository projects at Sandia National Laboratories including Waste Isolation Pilot Plant and Used Fuel Disposition. MoMaS benchmark has three independent tests with easy, medium, and hard chemical complexity. This paper demonstrates how PFLOTRAN is applied to this benchmark exercise and shows results of the easy benchmark test case which includes mixing of aqueous components and surface complexation. Surface complexations consist of monodentate and bidentate reactions which introduces difficulty in defining selectivity coefficient if the reaction applies to a bulk reference volume. The selectivity coefficient becomes porosity dependent for bidentate reaction in heterogeneous porous media. The benchmark is solved by PFLOTRAN with minimal modification to address the issue and unit conversions were made properly to suit PFLOTRAN.

Sensitivity Analysis of OECD Benchmark Tests in BISON

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Gamble, Kyle; Schmidt, Rodney C.

2015-09-01

This report summarizes a NEAMS (Nuclear Energy Advanced Modeling and Simulation) project focused on sensitivity analysis of a fuels performance benchmark problem. The benchmark problem was defined by the Uncertainty Analysis in Modeling working group of the Nuclear Science Committee, part of the Nuclear Energy Agency of the Organization for Economic Cooperation and Development (OECD ). The benchmark problem involv ed steady - state behavior of a fuel pin in a Pressurized Water Reactor (PWR). The problem was created in the BISON Fuels Performance code. Dakota was used to generate and analyze 300 samples of 17 input parameters defining coremore » boundary conditions, manuf acturing tolerances , and fuel properties. There were 24 responses of interest, including fuel centerline temperatures at a variety of locations and burnup levels, fission gas released, axial elongation of the fuel pin, etc. Pearson and Spearman correlatio n coefficients and Sobol' variance - based indices were used to perform the sensitivity analysis. This report summarizes the process and presents results from this study.« less

NRL 1989 Beam Propagation Studies in Support of the ATA Multi-Pulse Propagation Experiment

DTIC Science & Technology

1990-08-31

papers presented here were all written prior to the completion of the experiment. The first of these papers presents simulation results which modeled ...beam stability and channel evolution for an entire five pulse burst. The second paper describes a new air chemistry model used in the SARLAC...Experiment: A new air chemistry model for use in the propagation codes simulating the MPPE was developed by making analytic fits to benchmark runs with

Introduction to the IWA task group on biofilm modeling.

PubMed

Noguera, D R; Morgenroth, E

2004-01-01

An International Water Association (IWA) Task Group on Biofilm Modeling was created with the purpose of comparatively evaluating different biofilm modeling approaches. The task group developed three benchmark problems for this comparison, and used a diversity of modeling techniques that included analytical, pseudo-analytical, and numerical solutions to the biofilm problems. Models in one, two, and three dimensional domains were also compared. The first benchmark problem (BM1) described a monospecies biofilm growing in a completely mixed reactor environment and had the purpose of comparing the ability of the models to predict substrate fluxes and concentrations for a biofilm system of fixed total biomass and fixed biomass density. The second problem (BM2) represented a situation in which substrate mass transport by convection was influenced by the hydrodynamic conditions of the liquid in contact with the biofilm. The third problem (BM3) was designed to compare the ability of the models to simulate multispecies and multisubstrate biofilms. These three benchmark problems allowed identification of the specific advantages and disadvantages of each modeling approach. A detailed presentation of the comparative analyses for each problem is provided elsewhere in these proceedings.

Identification of fuel cycle simulator functionalities for analysis of transition to a new fuel cycle

DOE PAGES

Brown, Nicholas R.; Carlsen, Brett W.; Dixon, Brent W.; ...

2016-06-09

Dynamic fuel cycle simulation tools are intended to model holistic transient nuclear fuel cycle scenarios. As with all simulation tools, fuel cycle simulators require verification through unit tests, benchmark cases, and integral tests. Model validation is a vital aspect as well. Although compara-tive studies have been performed, there is no comprehensive unit test and benchmark library for fuel cycle simulator tools. The objective of this paper is to identify the must test functionalities of a fuel cycle simulator tool within the context of specific problems of interest to the Fuel Cycle Options Campaign within the U.S. Department of Energy smore » Office of Nuclear Energy. The approach in this paper identifies the features needed to cover the range of promising fuel cycle options identified in the DOE-NE Fuel Cycle Evaluation and Screening (E&S) and categorizes these features to facilitate prioritization. Features were categorized as essential functions, integrating features, and exemplary capabilities. One objective of this paper is to propose a library of unit tests applicable to each of the essential functions. Another underlying motivation for this paper is to encourage an international dialog on the functionalities and standard test methods for fuel cycle simulator tools.« less

Benchmarking of relative permeability

NASA Astrophysics Data System (ADS)

DiCarlo, D. A.

2017-12-01

Relative permeability is the key relation in terms of multi-phase flow through porous media. There are hundreds of published relative permeability curves for various media, some classic (Oak 90 and 91), some contradictory. This can lead to a confusing situation if one is trying to benchmark simulation results to "experimental data". Coming from the experimental side, I have found that modelers have too much trust in relative permeability data sets. In this talk, I will discuss reasons for discrepancies within and between data sets, and give guidance on which portions of the data sets are most solid in terms of matching through models.

Development of Benchmark Examples for Delamination Onset and Fatigue Growth Prediction

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2011-01-01

An approach for assessing the delamination propagation and growth capabilities in commercial finite element codes was developed and demonstrated for the Virtual Crack Closure Technique (VCCT) implementations in ABAQUS. The Double Cantilever Beam (DCB) specimen was chosen as an example. First, benchmark results to assess delamination propagation capabilities under static loading were created using models simulating specimens with different delamination lengths. For each delamination length modeled, the load and displacement at the load point were monitored. The mixed-mode strain energy release rate components were calculated along the delamination front across the width of the specimen. A failure index was calculated by correlating the results with the mixed-mode failure criterion of the graphite/epoxy material. The calculated critical loads and critical displacements for delamination onset for each delamination length modeled were used as a benchmark. The load/displacement relationship computed during automatic propagation should closely match the benchmark case. Second, starting from an initially straight front, the delamination was allowed to propagate based on the algorithms implemented in the commercial finite element software. The load-displacement relationship obtained from the propagation analysis results and the benchmark results were compared. Good agreements could be achieved by selecting the appropriate input parameters, which were determined in an iterative procedure.

Saturn Dynamo Model (Invited)

NASA Astrophysics Data System (ADS)

Glatzmaier, G. A.

2010-12-01

There has been considerable interest during the past few years about the banded zonal winds and global magnetic field on Saturn (and Jupiter). Questions regarding the depth to which the intense winds extend below the surface and the role they play in maintaining the dynamo continue to be debated. The types of computer models employed to address these questions fall into two main classes: general circulation models (GCMs) based on hydrostatic shallow-water assumptions from the atmospheric and ocean modeling communities and global non-hydrostatic deep convection models from the geodynamo and solar dynamo communities. The latter class can be further divided into Boussinesq models, which do not account for density stratification, and anelastic models, which do. Recent efforts to convert GCMs to deep circulation anelastic models have succeeded in producing fluid flows similar to those obtained from the original deep convection anelastic models. We describe results from one of the original anelastic convective dynamo simulations and compare them to a recent anelastic dynamo benchmark for giant gas planets. This benchmark is based on a polytropic reference state that spans five density scale heights with a radius and rotation rate similar to those of our solar system gas giants. The resulting magnetic Reynolds number is about 3000. Better spatial resolution will be required to produce more realistic predictions that capture the effects of both the density and electrical conductivity stratifications and include enough of the turbulent kinetic energy spectrum. Important additional physics may also be needed in the models. However, the basic models used in all simulation studies of the global dynamics of giant planets will hopefully first be validated by doing these simpler benchmarks.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnold H. Kritz

PTRANSP, which is the predictive version of the TRANSP code, was developed in a collaborative effort involving the Princeton Plasma Physics Laboratory, General Atomics Corporation, Lawrence Livermore National Laboratory, and Lehigh University. The PTRANSP/TRANSP suite of codes is the premier integrated tokamak modeling software in the United States. A production service for PTRANSP/TRANSP simulations is maintained at the Princeton Plasma Physics Laboratory; the server has a simple command line client interface and is subscribed to by about 100 researchers from tokamak projects in the US, Europe, and Asia. This service produced nearly 13000 PTRANSP/TRANSP simulations in the four year periodmore » FY 2005 through FY 2008. Major archives of TRANSP results are maintained at PPPL, MIT, General Atomics, and JET. Recent utilization, counting experimental analysis simulations as well as predictive simulations, more than doubled from slightly over 2000 simulations per year in FY 2005 and FY 2006 to over 4300 simulations per year in FY 2007 and FY 2008. PTRANSP predictive simulations applied to ITER increased eight fold from 30 simulations per year in FY 2005 and FY 2006 to 240 simulations per year in FY 2007 and FY 2008, accounting for more than half of combined PTRANSP/TRANSP service CPU resource utilization in FY 2008. PTRANSP studies focused on ITER played a key role in journal articles. Examples of validation studies carried out for momentum transport in PTRANSP simulations were presented at the 2008 IAEA conference. The increase in number of PTRANSP simulations has continued (more than 7000 TRANSP/PTRANSP simulations in 2010) and results of PTRANSP simulations appear in conference proceedings, for example the 2010 IAEA conference, and in peer reviewed papers. PTRANSP provides a bridge to the Fusion Simulation Program (FSP) and to the future of integrated modeling. Through years of widespread usage, each of the many parts of the PTRANSP suite of codes has been thoroughly validated against experimental data and benchmarked against other codes. At the same time, architectural modernizations are improving the modularity of the PTRANSP code base. The NUBEAM neutral beam and fusion products fast ion model, the Plasma State data repository (developed originally in the SWIM SciDAC project and adapted for use in PTRANSP), and other components are already shared with the SWIM, FACETS, and CPES SciDAC FSP prototype projects. Thus, the PTRANSP code is already serving as a bridge between our present integrated modeling capability and future capability. As the Fusion Simulation Program builds toward the facility currently available in the PTRANSP suite of codes, early versions of the FSP core plasma model will need to be benchmarked against the PTRANSP simulations. This will be necessary to build user confidence in FSP, but this benchmarking can only be done if PTRANSP itself is maintained and developed.« less

International benchmarking of longitudinal train dynamics simulators: results

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin; Chang, Chongyi; Guo, Gang; Sakalo, Alexey; Wei, Wei; Zhao, Xubao; Burgelman, Nico; Wiersma, Pier; Chollet, Hugues; Sebes, Michel; Shamdani, Amir; Melzi, Stefano; Cheli, Federico; di Gialleonardo, Egidio; Bosso, Nicola; Zampieri, Nicolò; Luo, Shihui; Wu, Honghua; Kaza, Guy-Léon

2018-03-01

This paper presents the results of the International Benchmarking of Longitudinal Train Dynamics Simulators which involved participation of nine simulators (TABLDSS, UM, CRE-LTS, TDEAS, PoliTo, TsDyn, CARS, BODYSIM and VOCO) from six countries. Longitudinal train dynamics results and computing time of four simulation cases are presented and compared. The results show that all simulators had basic agreement in simulations of locomotive forces, resistance forces and track gradients. The major differences among different simulators lie in the draft gear models. TABLDSS, UM, CRE-LTS, TDEAS, TsDyn and CARS had general agreement in terms of the in-train forces; minor differences exist as reflections of draft gear model variations. In-train force oscillations were observed in VOCO due to the introduction of wheel-rail contact. In-train force instabilities were sometimes observed in PoliTo and BODYSIM due to the velocity controlled transitional characteristics which could have generated unreasonable transitional stiffness. Regarding computing time per train operational second, the following list is in order of increasing computing speed: VOCO, TsDyn, PoliTO, CARS, BODYSIM, UM, TDEAS, CRE-LTS and TABLDSS (fastest); all simulators except VOCO, TsDyn and PoliTo achieved faster speeds than real-time simulations. Similarly, regarding computing time per integration step, the computing speeds in order are: CRE-LTS, VOCO, CARS, TsDyn, UM, TABLDSS and TDEAS (fastest).

Accelerating cardiac bidomain simulations using graphics processing units.

PubMed

Neic, A; Liebmann, M; Hoetzl, E; Mitchell, L; Vigmond, E J; Haase, G; Plank, G

2012-08-01

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6-20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20 GPUs, 476 CPU cores were required on a national supercomputing facility.

Accelerating Cardiac Bidomain Simulations Using Graphics Processing Units

PubMed Central

Neic, Aurel; Liebmann, Manfred; Hoetzl, Elena; Mitchell, Lawrence; Vigmond, Edward J.; Haase, Gundolf

2013-01-01

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6–20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20GPUs, 476 CPU cores were required on a national supercomputing facility. PMID:22692867

Thermal modeling with solid/liquid phase change of the thermal energy storage experiment

NASA Technical Reports Server (NTRS)

Skarda, J. Raymond Lee

1991-01-01

A thermal model which simulates combined conduction and phase change characteristics of thermal energy storage (TES) materials is presented. Both the model and results are presented for the purpose of benchmarking the conduction and phase change capabilities of recently developed and unvalidated microgravity TES computer programs. Specifically, operation of TES-1 is simulated. A two-dimensional SINDA85 model of the TES experiment in cylindrical coordinates was constructed. The phase change model accounts for latent heat stored in, or released from, a node undergoing melting and freezing.

Benchmarking novel approaches for modelling species range dynamics

PubMed Central

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H.; Moore, Kara A.; Zimmermann, Niklaus E.

2016-01-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species’ range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species’ response to climate change but also emphasise several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. PMID:26872305

Benchmarking novel approaches for modelling species range dynamics.

PubMed

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

2016-08-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. © 2016 John Wiley & Sons Ltd.

PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets.

PubMed

Yu, Jinchao; Guerois, Raphaël

2016-12-15

Protein-protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models. We explored how we could benefit from comparative modelling of unbound subunits to expand docking benchmark datasets. Starting from a collection of 3157 non-redundant, high X-ray resolution heterodimers, we developed the PPI4DOCK benchmark containing 1417 docking targets based on unbound homology models. Rigid-body docking by Zdock showed that for 1208 cases (85.2%), at least one correct decoy was generated, emphasizing the efficiency of rigid-body docking in generating correct assemblies. Overall, the PPI4DOCK benchmark contains a large set of realistic cases and provides new ground for assessing docking and scoring methodologies. Benchmark sets can be downloaded from http://biodev.cea.fr/interevol/ppi4dock/ CONTACT: guerois@cea.frSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Nonlinear model updating applied to the IMAC XXXII Round Robin benchmark system

NASA Astrophysics Data System (ADS)

Kurt, Mehmet; Moore, Keegan J.; Eriten, Melih; McFarland, D. Michael; Bergman, Lawrence A.; Vakakis, Alexander F.

2017-05-01

We consider the application of a new nonlinear model updating strategy to a computational benchmark system. The approach relies on analyzing system response time series in the frequency-energy domain by constructing both Hamiltonian and forced and damped frequency-energy plots (FEPs). The system parameters are then characterized and updated by matching the backbone branches of the FEPs with the frequency-energy wavelet transforms of experimental and/or computational time series. The main advantage of this method is that no nonlinearity model is assumed a priori, and the system model is updated solely based on simulation and/or experimental measured time series. By matching the frequency-energy plots of the benchmark system and its reduced-order model, we show that we are able to retrieve the global strongly nonlinear dynamics in the frequency and energy ranges of interest, identify bifurcations, characterize local nonlinearities, and accurately reconstruct time series. We apply the proposed methodology to a benchmark problem, which was posed to the system identification community prior to the IMAC XXXII (2014) and XXXIII (2015) Conferences as a "Round Robin Exercise on Nonlinear System Identification". We show that we are able to identify the parameters of the non-linear element in the problem with a priori knowledge about its position.

Benchmark Simulations of the Thermal-Hydraulic Responses during EBR-II Inherent Safety Tests using SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Rui; Sumner, Tyler S.

2016-04-17

An advanced system analysis tool SAM is being developed for fast-running, improved-fidelity, and whole-plant transient analyses at Argonne National Laboratory under DOE-NE’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. As an important part of code development, companion validation activities are being conducted to ensure the performance and validity of the SAM code. This paper presents the benchmark simulations of two EBR-II tests, SHRT-45R and BOP-302R, whose data are available through the support of DOE-NE’s Advanced Reactor Technology (ART) program. The code predictions of major primary coolant system parameter are compared with the test results. Additionally, the SAS4A/SASSYS-1 code simulationmore » results are also included for a code-to-code comparison.« less

A Uranium Bioremediation Reactive Transport Benchmark

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yabusaki, Steven B.; Sengor, Sevinc; Fang, Yilin

A reactive transport benchmark problem set has been developed based on in situ uranium bio-immobilization experiments that have been performed at a former uranium mill tailings site in Rifle, Colorado, USA. Acetate-amended groundwater stimulates indigenous microorganisms to catalyze the reduction of U(VI) to a sparingly soluble U(IV) mineral. The interplay between the flow, acetate loading periods and rates, microbially-mediated and geochemical reactions leads to dynamic behavior in metal- and sulfate-reducing bacteria, pH, alkalinity, and reactive mineral surfaces. The benchmark is based on an 8.5 m long one-dimensional model domain with constant saturated flow and uniform porosity. The 159-day simulation introducesmore » acetate and bromide through the upgradient boundary in 14-day and 85-day pulses separated by a 10 day interruption. Acetate loading is tripled during the second pulse, which is followed by a 50 day recovery period. Terminal electron accepting processes for goethite, phyllosilicate Fe(III), U(VI), and sulfate are modeled using Monod-type rate laws. Major ion geochemistry modeled includes mineral reactions, as well as aqueous and surface complexation reactions for UO2++, Fe++, and H+. In addition to the dynamics imparted by the transport of the acetate pulses, U(VI) behavior involves the interplay between bioreduction, which is dependent on acetate availability, and speciation-controlled surface complexation, which is dependent on pH, alkalinity and available surface complexation sites. The general difficulty of this benchmark is the large number of reactions (74), multiple rate law formulations, a multisite uranium surface complexation model, and the strong interdependency and sensitivity of the reaction processes. Results are presented for three simulators: HYDROGEOCHEM, PHT3D, and PHREEQC.« less

Nonparametric estimation of benchmark doses in environmental risk assessment

PubMed Central

Piegorsch, Walter W.; Xiong, Hui; Bhattacharya, Rabi N.; Lin, Lizhen

2013-01-01

Summary An important statistical objective in environmental risk analysis is estimation of minimum exposure levels, called benchmark doses (BMDs), that induce a pre-specified benchmark response in a dose-response experiment. In such settings, representations of the risk are traditionally based on a parametric dose-response model. It is a well-known concern, however, that if the chosen parametric form is misspecified, inaccurate and possibly unsafe low-dose inferences can result. We apply a nonparametric approach for calculating benchmark doses, based on an isotonic regression method for dose-response estimation with quantal-response data (Bhattacharya and Kong, 2007). We determine the large-sample properties of the estimator, develop bootstrap-based confidence limits on the BMDs, and explore the confidence limits’ small-sample properties via a short simulation study. An example from cancer risk assessment illustrates the calculations. PMID:23914133

Shift Verification and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G

2016-09-07

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over amore » burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.« less

Benchmark dose analysis via nonparametric regression modeling

PubMed Central

Piegorsch, Walter W.; Xiong, Hui; Bhattacharya, Rabi N.; Lin, Lizhen

2013-01-01

Estimation of benchmark doses (BMDs) in quantitative risk assessment traditionally is based upon parametric dose-response modeling. It is a well-known concern, however, that if the chosen parametric model is uncertain and/or misspecified, inaccurate and possibly unsafe low-dose inferences can result. We describe a nonparametric approach for estimating BMDs with quantal-response data based on an isotonic regression method, and also study use of corresponding, nonparametric, bootstrap-based confidence limits for the BMD. We explore the confidence limits’ small-sample properties via a simulation study, and illustrate the calculations with an example from cancer risk assessment. It is seen that this nonparametric approach can provide a useful alternative for BMD estimation when faced with the problem of parametric model uncertainty. PMID:23683057

Benchmarking and Modeling of a Conventional Mid-Size Car Using ALPHA (SAE Paper 2015-01-1140)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis (ALPHA) modeling tool was created by EPA to estimate greenhouse gas (GHG) emissions of light-duty vehicles. ALPHA is a physics-based, forward-looking, full vehicle computer simulation capable of analyzing various vehicle type...

Integrated Prediction and Mitigation Methods of Materials Damage and Lifetime Assessment during Plasma Operation and Various Instabilities in Fusion Devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hassanein, Ahmed

2015-03-31

This report describes implementation of comprehensive and integrated models to evaluate plasma material interactions during normal and abnormal plasma operations. The models in full3D simulations represent state-of-the art worldwide development with numerous benchmarking of various tokamak devices and plasma simulators. In addition, significant number of experimental work has been performed in our center for materials under extreme environment (CMUXE) at Purdue to benchmark the effect of intense particle and heat fluxes on plasma-facing components. This represents one-year worth of work and resulted in more than 23 Journal Publications and numerous conferences presentations. The funding has helped several students to obtainmore » their M.Sc. and Ph.D. degrees and many of them are now faculty members in US and around the world teaching and conducting fusion research. Our work has also been recognized through many awards.« less

Modelling anaerobic co-digestion in Benchmark Simulation Model No. 2: Parameter estimation, substrate characterisation and plant-wide integration.

PubMed

Arnell, Magnus; Astals, Sergi; Åmand, Linda; Batstone, Damien J; Jensen, Paul D; Jeppsson, Ulf

2016-07-01

Anaerobic co-digestion is an emerging practice at wastewater treatment plants (WWTPs) to improve the energy balance and integrate waste management. Modelling of co-digestion in a plant-wide WWTP model is a powerful tool to assess the impact of co-substrate selection and dose strategy on digester performance and plant-wide effects. A feasible procedure to characterise and fractionate co-substrates COD for the Benchmark Simulation Model No. 2 (BSM2) was developed. This procedure is also applicable for the Anaerobic Digestion Model No. 1 (ADM1). Long chain fatty acid inhibition was included in the ADM1 model to allow for realistic modelling of lipid rich co-substrates. Sensitivity analysis revealed that, apart from the biodegradable fraction of COD, protein and lipid fractions are the most important fractions for methane production and digester stability, with at least two major failure modes identified through principal component analysis (PCA). The model and procedure were tested on bio-methane potential (BMP) tests on three substrates, each rich on carbohydrates, proteins or lipids with good predictive capability in all three cases. This model was then applied to a plant-wide simulation study which confirmed the positive effects of co-digestion on methane production and total operational cost. Simulations also revealed the importance of limiting the protein load to the anaerobic digester to avoid ammonia inhibition in the digester and overloading of the nitrogen removal processes in the water train. In contrast, the digester can treat relatively high loads of lipid rich substrates without prolonged disturbances. Copyright © 2016 Elsevier Ltd. All rights reserved.

Properties of model-averaged BMDLs: a study of model averaging in dichotomous response risk estimation.

PubMed

Wheeler, Matthew W; Bailer, A John

2007-06-01

Model averaging (MA) has been proposed as a method of accounting for model uncertainty in benchmark dose (BMD) estimation. The technique has been used to average BMD dose estimates derived from dichotomous dose-response experiments, microbial dose-response experiments, as well as observational epidemiological studies. While MA is a promising tool for the risk assessor, a previous study suggested that the simple strategy of averaging individual models' BMD lower limits did not yield interval estimators that met nominal coverage levels in certain situations, and this performance was very sensitive to the underlying model space chosen. We present a different, more computationally intensive, approach in which the BMD is estimated using the average dose-response model and the corresponding benchmark dose lower bound (BMDL) is computed by bootstrapping. This method is illustrated with TiO(2) dose-response rat lung cancer data, and then systematically studied through an extensive Monte Carlo simulation. The results of this study suggest that the MA-BMD, estimated using this technique, performs better, in terms of bias and coverage, than the previous MA methodology. Further, the MA-BMDL achieves nominal coverage in most cases, and is superior to picking the "best fitting model" when estimating the benchmark dose. Although these results show utility of MA for benchmark dose risk estimation, they continue to highlight the importance of choosing an adequate model space as well as proper model fit diagnostics.

Visco-Resistive MHD Modeling Benchmark of Forced Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Beidler, M. T.; Hegna, C. C.; Sovinec, C. R.; Callen, J. D.; Ferraro, N. M.

2016-10-01

The presence of externally-applied 3D magnetic fields can affect important phenomena in tokamaks, including mode locking, disruptions, and edge localized modes. External fields penetrate into the plasma and can lead to forced magnetic reconnection (FMR), and hence magnetic islands, on resonant surfaces if the local plasma rotation relative to the external field is slow. Preliminary visco-resistive MHD simulations of FMR in a slab geometry are consistent with theory. Specifically, linear simulations exhibit proper scaling of the penetrated field with resistivity, viscosity, and flow, and nonlinear simulations exhibit a bifurcation from a flow-screened to a field-penetrated, magnetic island state as the external field is increased, due to the 3D electromagnetic force. These results will be compared to simulations of FMR in a circular cross-section, cylindrical geometry by way of a benchmark between the NIMROD and M3D-C1 extended-MHD codes. Because neither this geometry nor the MHD model has the physics of poloidal flow damping, the theory of will be expanded to include poloidal flow effects. The resulting theory will be tested with linear and nonlinear simulations that vary the resistivity, viscosity, flow, and external field. Supported by OFES DoE Grants DE-FG02-92ER54139, DE-FG02-86ER53218, DE-AC02-09CH11466, and the SciDAC Center for Extended MHD Modeling.

Competency based training in robotic surgery: benchmark scores for virtual reality robotic simulation.

PubMed

Raison, Nicholas; Ahmed, Kamran; Fossati, Nicola; Buffi, Nicolò; Mottrie, Alexandre; Dasgupta, Prokar; Van Der Poel, Henk

2017-05-01

To develop benchmark scores of competency for use within a competency based virtual reality (VR) robotic training curriculum. This longitudinal, observational study analysed results from nine European Association of Urology hands-on-training courses in VR simulation. In all, 223 participants ranging from novice to expert robotic surgeons completed 1565 exercises. Competency was set at 75% of the mean expert score. Benchmark scores for all general performance metrics generated by the simulator were calculated. Assessment exercises were selected by expert consensus and through learning-curve analysis. Three basic skill and two advanced skill exercises were identified. Benchmark scores based on expert performance offered viable targets for novice and intermediate trainees in robotic surgery. Novice participants met the competency standards for most basic skill exercises; however, advanced exercises were significantly more challenging. Intermediate participants performed better across the seven metrics but still did not achieve the benchmark standard in the more difficult exercises. Benchmark scores derived from expert performances offer relevant and challenging scores for trainees to achieve during VR simulation training. Objective feedback allows both participants and trainers to monitor educational progress and ensures that training remains effective. Furthermore, the well-defined goals set through benchmarking offer clear targets for trainees and enable training to move to a more efficient competency based curriculum. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

Using HFire for spatial modeling of fire in shrublands

Treesearch

Seth H. Peterson; Marco E. Morais; Jean M. Carlson; Philip E. Dennison; Dar A. Roberts; Max A. Moritz; David R. Weise

2009-01-01

An efficient raster fire-spread model named HFire is introduced. HFire can simulate single-fire events or long-term fire regimes, using the same fire-spread algorithm. This paper describes the HFire algorithm, benchmarks the model using a standard set of tests developed for FARSITE, and compares historical and predicted fire spread perimeters for three southern...

SCOUT: A Fast Monte-Carlo Modeling Tool of Scintillation Camera Output

PubMed Central

Hunter, William C. J.; Barrett, Harrison H.; Lewellen, Thomas K.; Miyaoka, Robert S.; Muzi, John P.; Li, Xiaoli; McDougald, Wendy; MacDonald, Lawrence R.

2011-01-01

We have developed a Monte-Carlo photon-tracking and readout simulator called SCOUT to study the stochastic behavior of signals output from a simplified rectangular scintillation-camera design. SCOUT models the salient processes affecting signal generation, transport, and readout. Presently, we compare output signal statistics from SCOUT to experimental results for both a discrete and a monolithic camera. We also benchmark the speed of this simulation tool and compare it to existing simulation tools. We find this modeling tool to be relatively fast and predictive of experimental results. Depending on the modeled camera geometry, we found SCOUT to be 4 to 140 times faster than other modeling tools. PMID:22072297

SCOUT: a fast Monte-Carlo modeling tool of scintillation camera output†

PubMed Central

Hunter, William C J; Barrett, Harrison H.; Muzi, John P.; McDougald, Wendy; MacDonald, Lawrence R.; Miyaoka, Robert S.; Lewellen, Thomas K.

2013-01-01

We have developed a Monte-Carlo photon-tracking and readout simulator called SCOUT to study the stochastic behavior of signals output from a simplified rectangular scintillation-camera design. SCOUT models the salient processes affecting signal generation, transport, and readout of a scintillation camera. Presently, we compare output signal statistics from SCOUT to experimental results for both a discrete and a monolithic camera. We also benchmark the speed of this simulation tool and compare it to existing simulation tools. We find this modeling tool to be relatively fast and predictive of experimental results. Depending on the modeled camera geometry, we found SCOUT to be 4 to 140 times faster than other modeling tools. PMID:23640136

ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Highly Efficient Lattice Boltzmann Model for Compressible Fluids: Two-Dimensional Case

NASA Astrophysics Data System (ADS)

Chen, Feng; Xu, Ai-Guo; Zhang, Guang-Cai; Gan, Yan-Biao; Cheng, Tao; Li, Ying-Jun

2009-10-01

We present a highly efficient lattice Boltzmann model for simulating compressible flows. This model is based on the combination of an appropriate finite difference scheme, a 16-discrete-velocity model [Kataoka and Tsutahara, Phys. Rev. E 69 (2004) 035701(R)] and reasonable dispersion and dissipation terms. The dispersion term effectively reduces the oscillation at the discontinuity and enhances numerical precision. The dissipation term makes the new model more easily meet with the von Neumann stability condition. This model works for both high-speed and low-speed flows with arbitrary specific-heat-ratio. With the new model simulation results for the well-known benchmark problems get a high accuracy compared with the analytic or experimental ones. The used benchmark tests include (i) Shock tubes such as the Sod, Lax, Sjogreen, Colella explosion wave, and collision of two strong shocks, (ii) Regular and Mach shock reflections, and (iii) Shock wave reaction on cylindrical bubble problems. With a more realistic equation of state or free-energy functional, the new model has the potential tostudy the complex procedure of shock wave reaction on porous materials.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Target Lagrangian kinematic simulation for particle-laden flows.

PubMed

Murray, S; Lightstone, M F; Tullis, S

2016-09-01

The target Lagrangian kinematic simulation method was motivated as a stochastic Lagrangian particle model that better synthesizes turbulence structure, relative to stochastic separated flow models. By this method, the trajectories of particles are constructed according to synthetic turbulent-like fields, which conform to a target Lagrangian integral timescale. In addition to recovering the expected Lagrangian properties of fluid tracers, this method is shown to reproduce the crossing trajectories and continuity effects, in agreement with an experimental benchmark.

Haptic simulation framework for determining virtual dental occlusion.

PubMed

Wu, Wen; Chen, Hui; Cen, Yuhai; Hong, Yang; Khambay, Balvinder; Heng, Pheng Ann

2017-04-01

The surgical treatment of many dentofacial deformities is often complex due to its three-dimensional nature. To determine the dental occlusion in the most stable position is essential for the success of the treatment. Computer-aided virtual planning on individualized patient-specific 3D model can help formulate the surgical plan and predict the surgical change. However, in current computer-aided planning systems, it is not possible to determine the dental occlusion of the digital models in the intuitive way during virtual surgical planning because of absence of haptic feedback. In this paper, a physically based haptic simulation framework is proposed, which can provide surgeons with the intuitive haptic feedback to determine the dental occlusion of the digital models in their most stable position. To provide the physically realistic force feedback when the dental models contact each other during the searching process, the contact model is proposed to describe the dynamic and collision properties of the dental models during the alignment. The simulated impulse/contact-based forces are integrated into the unified simulation framework. A validation study has been conducted on fifteen sets of virtual dental models chosen at random and covering a wide range of the dental relationships found clinically. The dental occlusions obtained by an expert were employed as a benchmark to compare the virtual occlusion results. The mean translational and angular deviations of the virtual occlusion results from the benchmark were small. The experimental results show the validity of our method. The simulated forces can provide valuable insights to determine the virtual dental occlusion. The findings of this work and the validation of proposed concept lead the way for full virtual surgical planning on patient-specific virtual models allowing fully customized treatment plans for the surgical correction of dentofacial deformities.

Anharmonic Vibrational Spectroscopy on Metal Transition Complexes

NASA Astrophysics Data System (ADS)

Latouche, Camille; Bloino, Julien; Barone, Vincenzo

2014-06-01

Advances in hardware performance and the availability of efficient and reliable computational models have made possible the application of computational spectroscopy to ever larger molecular systems. The systematic interpretation of experimental data and the full characterization of complex molecules can then be facilitated. Focusing on vibrational spectroscopy, several approaches have been proposed to simulate spectra beyond the double harmonic approximation, so that more details become available. However, a routine use of such tools requires the preliminary definition of a valid protocol with the most appropriate combination of electronic structure and nuclear calculation models. Several benchmark of anharmonic calculations frequency have been realized on organic molecules. Nevertheless, benchmarks of organometallics or inorganic metal complexes at this level are strongly lacking despite the interest of these systems due to their strong emission and vibrational properties. Herein we report the benchmark study realized with anharmonic calculations on simple metal complexes, along with some pilot applications on systems of direct technological or biological interest.

Entropic multirelaxation-time lattice Boltzmann method for moving and deforming geometries in three dimensions

NASA Astrophysics Data System (ADS)

Dorschner, B.; Chikatamarla, S. S.; Karlin, I. V.

2017-06-01

Entropic lattice Boltzmann methods have been developed to alleviate intrinsic stability issues of lattice Boltzmann models for under-resolved simulations. Its reliability in combination with moving objects was established for various laminar benchmark flows in two dimensions in our previous work [B. Dorschner, S. Chikatamarla, F. Bösch, and I. Karlin, J. Comput. Phys. 295, 340 (2015), 10.1016/j.jcp.2015.04.017] as well as for three-dimensional one-way coupled simulations of engine-type geometries in B . Dorschner, F. Bösch, S. Chikatamarla, K. Boulouchos, and I. Karlin [J. Fluid Mech. 801, 623 (2016), 10.1017/jfm.2016.448] for flat moving walls. The present contribution aims to fully exploit the advantages of entropic lattice Boltzmann models in terms of stability and accuracy and extends the methodology to three-dimensional cases, including two-way coupling between fluid and structure and then turbulence and deforming geometries. To cover this wide range of applications, the classical benchmark of a sedimenting sphere is chosen first to validate the general two-way coupling algorithm. Increasing the complexity, we subsequently consider the simulation of a plunging SD7003 airfoil in the transitional regime at a Reynolds number of Re =40 000 and, finally, to access the model's performance for deforming geometries, we conduct a two-way coupled simulation of a self-propelled anguilliform swimmer. These simulations confirm the viability of the new fluid-structure interaction lattice Boltzmann algorithm to simulate flows of engineering relevance.

Benchmark Evaluation of HTR-PROTEUS Pebble Bed Experimental Program

DOE PAGES

Bess, John D.; Montierth, Leland; Köberl, Oliver; ...

2014-10-09

Benchmark models were developed to evaluate 11 critical core configurations of the HTR-PROTEUS pebble bed experimental program. Various additional reactor physics measurements were performed as part of this program; currently only a total of 37 absorber rod worth measurements have been evaluated as acceptable benchmark experiments for Cores 4, 9, and 10. Dominant uncertainties in the experimental keff for all core configurations come from uncertainties in the ²³⁵U enrichment of the fuel, impurities in the moderator pebbles, and the density and impurity content of the radial reflector. Calculations of k eff with MCNP5 and ENDF/B-VII.0 neutron nuclear data aremore » greater than the benchmark values but within 1% and also within the 3σ uncertainty, except for Core 4, which is the only randomly packed pebble configuration. Repeated calculations of k eff with MCNP6.1 and ENDF/B-VII.1 are lower than the benchmark values and within 1% (~3σ) except for Cores 5 and 9, which calculate lower than the benchmark eigenvalues within 4σ. The primary difference between the two nuclear data libraries is the adjustment of the absorption cross section of graphite. Simulations of the absorber rod worth measurements are within 3σ of the benchmark experiment values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments.« less

A Systems Approach to Scalable Transportation Network Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perumalla, Kalyan S

2006-01-01

Emerging needs in transportation network modeling and simulation are raising new challenges with respect to scal-ability of network size and vehicular traffic intensity, speed of simulation for simulation-based optimization, and fidel-ity of vehicular behavior for accurate capture of event phe-nomena. Parallel execution is warranted to sustain the re-quired detail, size and speed. However, few parallel simulators exist for such applications, partly due to the challenges underlying their development. Moreover, many simulators are based on time-stepped models, which can be computationally inefficient for the purposes of modeling evacuation traffic. Here an approach is presented to de-signing a simulator with memory andmore » speed efficiency as the goals from the outset, and, specifically, scalability via parallel execution. The design makes use of discrete event modeling techniques as well as parallel simulation meth-ods. Our simulator, called SCATTER, is being developed, incorporating such design considerations. Preliminary per-formance results are presented on benchmark road net-works, showing scalability to one million vehicles simu-lated on one processor.« less

Closed-Loop Neuromorphic Benchmarks

PubMed Central

Stewart, Terrence C.; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

2015-01-01

Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of “minimal” simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

Data Intensive Systems (DIS) Benchmark Performance Summary

DTIC Science & Technology

2003-08-01

models assumed by today’s conventional architectures. Such applications include model- based Automatic Target Recognition (ATR), synthetic aperture...radar (SAR) codes, large scale dynamic databases/battlefield integration, dynamic sensor- based processing, high-speed cryptanalysis, high speed...distributed interactive and data intensive simulations, data-oriented problems characterized by pointer- based and other highly irregular data structures

FDA Benchmark Medical Device Flow Models for CFD Validation.

PubMed

Malinauskas, Richard A; Hariharan, Prasanna; Day, Steven W; Herbertson, Luke H; Buesen, Martin; Steinseifer, Ulrich; Aycock, Kenneth I; Good, Bryan C; Deutsch, Steven; Manning, Keefe B; Craven, Brent A

Computational fluid dynamics (CFD) is increasingly being used to develop blood-contacting medical devices. However, the lack of standardized methods for validating CFD simulations and blood damage predictions limits its use in the safety evaluation of devices. Through a U.S. Food and Drug Administration (FDA) initiative, two benchmark models of typical device flow geometries (nozzle and centrifugal blood pump) were tested in multiple laboratories to provide experimental velocities, pressures, and hemolysis data to support CFD validation. In addition, computational simulations were performed by more than 20 independent groups to assess current CFD techniques. The primary goal of this article is to summarize the FDA initiative and to report recent findings from the benchmark blood pump model study. Discrepancies between CFD predicted velocities and those measured using particle image velocimetry most often occurred in regions of flow separation (e.g., downstream of the nozzle throat, and in the pump exit diffuser). For the six pump test conditions, 57% of the CFD predictions of pressure head were within one standard deviation of the mean measured values. Notably, only 37% of all CFD submissions contained hemolysis predictions. This project aided in the development of an FDA Guidance Document on factors to consider when reporting computational studies in medical device regulatory submissions. There is an accompanying podcast available for this article. Please visit the journal's Web site (www.asaiojournal.com) to listen.

Numerical simulation of three-component multiphase flows at high density and viscosity ratios using lattice Boltzmann methods

NASA Astrophysics Data System (ADS)

Haghani Hassan Abadi, Reza; Fakhari, Abbas; Rahimian, Mohammad Hassan

2018-03-01

In this paper, we propose a multiphase lattice Boltzmann model for numerical simulation of ternary flows at high density and viscosity ratios free from spurious velocities. The proposed scheme, which is based on the phase-field modeling, employs the Cahn-Hilliard theory to track the interfaces among three different fluid components. Several benchmarks, such as the spreading of a liquid lens, binary droplets, and head-on collision of two droplets in binary- and ternary-fluid systems, are conducted to assess the reliability and accuracy of the model. The proposed model can successfully simulate both partial and total spreadings while reducing the parasitic currents to the machine precision.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinilla, Maria Isabel

This report seeks to study and benchmark code predictions against experimental data; determine parameters to match MCNP-simulated detector response functions to experimental stilbene measurements; add stilbene processing capabilities to DRiFT; and improve NEUANCE detector array modeling and analysis using new MCNP6 and DRiFT features.

On the predictability of land surface fluxes from meteorological variables

NASA Astrophysics Data System (ADS)

Haughton, Ned; Abramowitz, Gab; Pitman, Andy J.

2018-01-01

Previous research has shown that land surface models (LSMs) are performing poorly when compared with relatively simple empirical models over a wide range of metrics and environments. Atmospheric driving data appear to provide information about land surface fluxes that LSMs are not fully utilising. Here, we further quantify the information available in the meteorological forcing data that are used by LSMs for predicting land surface fluxes, by interrogating FLUXNET data, and extending the benchmarking methodology used in previous experiments. We show that substantial performance improvement is possible for empirical models using meteorological data alone, with no explicit vegetation or soil properties, thus setting lower bounds on a priori expectations on LSM performance. The process also identifies key meteorological variables that provide predictive power. We provide an ensemble of empirical benchmarks that are simple to reproduce and provide a range of behaviours and predictive performance, acting as a baseline benchmark set for future studies. We reanalyse previously published LSM simulations and show that there is more diversity between LSMs than previously indicated, although it remains unclear why LSMs are broadly performing so much worse than simple empirical models.

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, David (Editor); Barton, John (Editor); Lasinski, Thomas (Editor); Simon, Horst (Editor)

1993-01-01

A new set of benchmarks was developed for the performance evaluation of highly parallel supercomputers. These benchmarks consist of a set of kernels, the 'Parallel Kernels,' and a simulated application benchmark. Together they mimic the computation and data movement characteristics of large scale computational fluid dynamics (CFD) applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification - all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

Self-adaptive Fault-Tolerance of HLA-Based Simulations in the Grid Environment

NASA Astrophysics Data System (ADS)

Huang, Jijie; Chai, Xudong; Zhang, Lin; Li, Bo Hu

The objects of a HLA-based simulation can access model services to update their attributes. However, the grid server may be overloaded and refuse the model service to handle objects accesses. Because these objects have been accessed this model service during last simulation loop and their medium state are stored in this server, this may terminate the simulation. A fault-tolerance mechanism must be introduced into simulations. But the traditional fault-tolerance methods cannot meet the above needs because the transmission latency between a federate and the RTI in grid environment varies from several hundred milliseconds to several seconds. By adding model service URLs to the OMT and expanding the HLA services and model services with some interfaces, this paper proposes a self-adaptive fault-tolerance mechanism of simulations according to the characteristics of federates accessing model services. Benchmark experiments indicate that the expanded HLA/RTI can make simulations self-adaptively run in the grid environment.

Higher representations on the lattice: Numerical simulations, SU(2) with adjoint fermions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Del Debbio, Luigi; Patella, Agostino; Pica, Claudio

2010-05-01

We discuss the lattice formulation of gauge theories with fermions in arbitrary representations of the color group and present in detail the implementation of the hybrid Monte Carlo (HMC)/rational HMC algorithm for simulating dynamical fermions. We discuss the validation of the implementation through an extensive set of tests and the stability of simulations by monitoring the distribution of the lowest eigenvalue of the Wilson-Dirac operator. Working with two flavors of Wilson fermions in the adjoint representation, benchmark results for realistic lattice simulations are presented. Runs are performed on different lattice sizes ranging from 4{sup 3}x8 to 24{sup 3}x64 sites. Formore » the two smallest lattices we also report the measured values of benchmark mesonic observables. These results can be used as a baseline for rapid cross-checks of simulations in higher representations. The results presented here are the first steps toward more extensive investigations with controlled systematic errors, aiming at a detailed understanding of the phase structure of these theories, and of their viability as candidates for strong dynamics beyond the standard model.« less

Integrated Disposal Facility FY 2016: ILAW Verification and Validation of the eSTOMP Simulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Vicky L.; Bacon, Diana H.; Fang, Yilin

2016-05-13

This document describes two sets of simulations carried out to further verify and validate the eSTOMP simulator. In this report, a distinction is made between verification and validation, and the focus is on verifying eSTOMP through a series of published benchmarks on cementitious wastes, and validating eSTOMP based on a lysimeter experiment for the glassified waste. These activities are carried out within the context of a scientific view of validation that asserts that models can only be invalidated, and that model validation (and verification) is a subjective assessment.

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins.

PubMed

Li, Min; Zhang, John Z H

2017-03-08

The development of polarizable water models at coarse-grained (CG) levels is of much importance to CG molecular dynamics simulations of large biomolecular systems. In this work, we combined the newly developed two-bead multipole force field (TMFF) for proteins with the two-bead polarizable water models to carry out CG molecular dynamics simulations for benchmark proteins. In our simulations, two different two-bead polarizable water models are employed, the RTPW model representing five water molecules by Riniker et al. and the LTPW model representing four water molecules. The LTPW model is developed in this study based on the Martini three-bead polarizable water model. Our simulation results showed that the combination of TMFF with the LTPW model significantly stabilizes the protein's native structure in CG simulations, while the use of the RTPW model gives better agreement with all-atom simulations in predicting the residue-level fluctuation dynamics. Overall, the TMFF coupled with the two-bead polarizable water models enables one to perform an efficient and reliable CG dynamics study of the structural and functional properties of large biomolecules.

Validation of Tendril TrueHome Using Software-to-Software Comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maguire, Jeffrey B; Horowitz, Scott G; Moore, Nathan

This study performed comparative evaluation of EnergyPlus version 8.6 and Tendril TrueHome, two physics-based home energy simulation models, to identify differences in energy consumption predictions between the two programs and resolve discrepancies between them. EnergyPlus is considered a benchmark, best-in-class software tool for building energy simulation. This exercise sought to improve both software tools through additional evaluation/scrutiny.

A simulation study of thinning and fuel treatments on a wildland-urban interface in eastern Oregon, USA

Treesearch

Alan A. Ager; Andrew J. McMahan; James J. Barrett; Charles W. McHugh

2007-01-01

We simulated long-term forest management activities on 16,000-ha wildland-urban interface in the Blue Mountains near La Grande, Oregon. The study area is targeted for thinning and fuels treatments on both private and Federally managed lands to address forest health and sustainability concerns and reduce the risk of severe wildfire. We modeled number of benchmark...

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Inter-model analysis of tsunami-induced coastal currents

NASA Astrophysics Data System (ADS)

Lynett, Patrick J.; Gately, Kara; Wilson, Rick; Montoya, Luis; Arcas, Diego; Aytore, Betul; Bai, Yefei; Bricker, Jeremy D.; Castro, Manuel J.; Cheung, Kwok Fai; David, C. Gabriel; Dogan, Gozde Guney; Escalante, Cipriano; González-Vida, José Manuel; Grilli, Stephan T.; Heitmann, Troy W.; Horrillo, Juan; Kânoğlu, Utku; Kian, Rozita; Kirby, James T.; Li, Wenwen; Macías, Jorge; Nicolsky, Dmitry J.; Ortega, Sergio; Pampell-Manis, Alyssa; Park, Yong Sung; Roeber, Volker; Sharghivand, Naeimeh; Shelby, Michael; Shi, Fengyan; Tehranirad, Babak; Tolkova, Elena; Thio, Hong Kie; Velioğlu, Deniz; Yalçıner, Ahmet Cevdet; Yamazaki, Yoshiki; Zaytsev, Andrey; Zhang, Y. J.

2017-06-01

To help produce accurate and consistent maritime hazard products, the National Tsunami Hazard Mitigation Program organized a benchmarking workshop to evaluate the numerical modeling of tsunami currents. Thirteen teams of international researchers, using a set of tsunami models currently utilized for hazard mitigation studies, presented results for a series of benchmarking problems; these results are summarized in this paper. Comparisons focus on physical situations where the currents are shear and separation driven, and are thus de-coupled from the incident tsunami waveform. In general, we find that models of increasing physical complexity provide better accuracy, and that low-order three-dimensional models are superior to high-order two-dimensional models. Inside separation zones and in areas strongly affected by eddies, the magnitude of both model-data errors and inter-model differences can be the same as the magnitude of the mean flow. Thus, we make arguments for the need of an ensemble modeling approach for areas affected by large-scale turbulent eddies, where deterministic simulation may be misleading. As a result of the analyses presented herein, we expect that tsunami modelers now have a better awareness of their ability to accurately capture the physics of tsunami currents, and therefore a better understanding of how to use these simulation tools for hazard assessment and mitigation efforts.

A discrete-element model for viscoelastic deformation and fracture of glacial ice

NASA Astrophysics Data System (ADS)

Riikilä, T. I.; Tallinen, T.; Åström, J.; Timonen, J.

2015-10-01

A discrete-element model was developed to study the behavior of viscoelastic materials that are allowed to fracture. Applicable to many materials, the main objective of this analysis was to develop a model specifically for ice dynamics. A realistic model of glacial ice must include elasticity, brittle fracture and slow viscous deformations. Here the model is described in detail and tested with several benchmark simulations. The model was used to simulate various ice-specific applications with resulting flow rates that were compatible with Glen's law, and produced under fragmentation fragment-size distributions that agreed with the known analytical and experimental results.

The application of a Web-geographic information system for improving urban water cycle modelling.

PubMed

Mair, M; Mikovits, C; Sengthaler, M; Schöpf, M; Kinzel, H; Urich, C; Kleidorfer, M; Sitzenfrei, R; Rauch, W

2014-01-01

Research in urban water management has experienced a transition from traditional model applications to modelling water cycles as an integrated part of urban areas. This includes the interlinking of models of many research areas (e.g. urban development, socio-economy, urban water management). The integration and simulation is realized in newly developed frameworks (e.g. DynaMind and OpenMI) and often assumes a high knowledge in programming. This work presents a Web based urban water management modelling platform which simplifies the setup and usage of complex integrated models. The platform is demonstrated with a small application example on a case study within the Alpine region. The used model is a DynaMind model benchmarking the impact of newly connected catchments on the flooding behaviour of an existing combined sewer system. As a result the workflow of the user within a Web browser is demonstrated and benchmark results are shown. The presented platform hides implementation specific aspects behind Web services based technologies such that the user can focus on his main aim, which is urban water management modelling and benchmarking. Moreover, this platform offers a centralized data management, automatic software updates and access to high performance computers accessible with desktop computers and mobile devices.

Model benchmarking and reference signals for angled-beam shear wave ultrasonic nondestructive evaluation (NDE) inspections

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Hopkins, Deborah; Datuin, Marvin; Warchol, Mark; Warchol, Lyudmila; Forsyth, David S.; Buynak, Charlie; Lindgren, Eric A.

2017-02-01

For model benchmark studies, the accuracy of the model is typically evaluated based on the change in response relative to a selected reference signal. The use of a side drilled hole (SDH) in a plate was investigated as a reference signal for angled beam shear wave inspection for aircraft structure inspections of fastener sites. Systematic studies were performed with varying SDH depth and size, and varying the ultrasonic probe frequency, focal depth, and probe height. Increased error was observed with the simulation of angled shear wave beams in the near-field. Even more significant, asymmetry in real probes and the inherent sensitivity of signals in the near-field to subtle test conditions were found to provide a greater challenge with achieving model agreement. To achieve quality model benchmark results for this problem, it is critical to carefully align the probe with the part geometry, to verify symmetry in probe response, and ideally avoid using reference signals from the near-field response. Suggested reference signals for angled beam shear wave inspections include using the `through hole' corner specular reflection signal and the full skip' signal off of the far wall from the side drilled hole.

Streamlining DOD Acquisitions: Balancing Schedule with Complexity

DTIC Science & Technology

2006-09-01

from them has a distinct industrial flavor: streamlined processes, benchmarking, and business models . The requirements generation com- munity led by... model ), and the Department of the Navy assumed program lead. [Stable Program Inputs (-)] By 1984, the program goals included delivery of 913 V-22...they subsequently specified a crew of two. [Stable Program Input (-)] The contractor team won in a “fly-off” solely via modeling and simulation

Simulator for SUPO, a Benchmark Aqueous Homogeneous Reactor (AHR)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, Steven Karl; Determan, John C.

2015-10-14

A simulator has been developed for SUPO (Super Power) an aqueous homogeneous reactor (AHR) that operated at Los Alamos National Laboratory (LANL) from 1951 to 1974. During that period SUPO accumulated approximately 600,000 kWh of operation. It is considered the benchmark for steady-state operation of an AHR. The SUPO simulator was developed using the process that resulted in a simulator for an accelerator-driven subcritical system, which has been previously reported.

Manure nutrient management effects in the Leon River Watershed

USDA-ARS?s Scientific Manuscript database

The Leon River Watershed (LRW) in central Texas is a Benchmark and Special Emphasis watershed within the Conservation Effects Assessment Project (CEAP) located in central Texas. Model simulations from 1977 through 2006 were used to evaluate six manure nutrient management scenarios that reflect reali...

Progress in Unsteady Turbopump Flow Simulations Using Overset Grid Systems

NASA Technical Reports Server (NTRS)

Kiris, Cetin C.; Chan, William; Kwak, Dochan

2002-01-01

This viewgraph presentation provides information on unsteady flow simulations for the Second Generation RLV (Reusable Launch Vehicle) baseline turbopump. Three impeller rotations were simulated by using a 34.3 million grid points model. MPI/OpenMP hybrid parallelism and MLP shared memory parallelism has been implemented and benchmarked in INS3D, an incompressible Navier-Stokes solver. For RLV turbopump simulations a speed up of more than 30 times has been obtained. Moving boundary capability is obtained by using the DCF module. Scripting capability from CAD geometry to solution is developed. Unsteady flow simulations for advanced consortium impeller/diffuser by using a 39 million grid points model are currently underway. 1.2 impeller rotations are completed. The fluid/structure coupling is initiated.

SU-E-J-30: Benchmark Image-Based TCP Calculation for Evaluation of PTV Margins for Lung SBRT Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, M; Chetty, I; Zhong, H

2014-06-01

Purpose: Tumor control probability (TCP) calculated with accumulated radiation doses may help design appropriate treatment margins. Image registration errors, however, may compromise the calculated TCP. The purpose of this study is to develop benchmark CT images to quantify registration-induced errors in the accumulated doses and their corresponding TCP. Methods: 4DCT images were registered from end-inhale (EI) to end-exhale (EE) using a “demons” algorithm. The demons DVFs were corrected by an FEM model to get realistic deformation fields. The FEM DVFs were used to warp the EI images to create the FEM-simulated images. The two images combined with the FEM DVFmore » formed a benchmark model. Maximum intensity projection (MIP) images, created from the EI and simulated images, were used to develop IMRT plans. Two plans with 3 and 5 mm margins were developed for each patient. With these plans, radiation doses were recalculated on the simulated images and warped back to the EI images using the FEM DVFs to get the accumulated doses. The Elastix software was used to register the FEM-simulated images to the EI images. TCPs calculated with the Elastix-accumulated doses were compared with those generated by the FEM to get the TCP error of the Elastix registrations. Results: For six lung patients, the mean Elastix registration error ranged from 0.93 to 1.98 mm. Their relative dose errors in PTV were between 0.28% and 6.8% for 3mm margin plans, and between 0.29% and 6.3% for 5mm-margin plans. As the PTV margin reduced from 5 to 3 mm, the mean TCP error of the Elastix-reconstructed doses increased from 2.0% to 2.9%, and the mean NTCP errors decreased from 1.2% to 1.1%. Conclusion: Patient-specific benchmark images can be used to evaluate the impact of registration errors on the computed TCPs, and may help select appropriate PTV margins for lung SBRT patients.« less

A Benchmarking setup for Coupled Earthquake Cycle - Dynamic Rupture - Tsunami Simulations

NASA Astrophysics Data System (ADS)

Behrens, Joern; Bader, Michael; van Dinther, Ylona; Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Uphoff, Carsten; Vater, Stefan; Wollherr, Stephanie; van Zelst, Iris

2017-04-01

We developed a simulation framework for coupled physics-based earthquake rupture generation with tsunami propagation and inundation on a simplified subduction zone system for the project "Advanced Simulation of Coupled Earthquake and Tsunami Events" (ASCETE, funded by the Volkswagen Foundation). Here, we present a benchmarking setup that can be used for complex rupture models. The workflow begins with a 2D seismo-thermo-mechanical earthquake cycle model representing long term deformation along a planar, shallowly dipping subduction zone interface. Slip instabilities that approximate earthquakes arise spontaneously along the subduction zone interface in this model. The absolute stress field and material properties for a single slip event are used as initial conditions for a dynamic earthquake rupture model.The rupture simulation is performed with SeisSol, which uses an ADER discontinuous Galerkin discretization scheme with an unstructured tetrahedral mesh. The seafloor displacements resulting from this rupture are transferred to the tsunami model with a simple coastal run-up profile. An adaptive mesh discretizing the shallow water equations with a Runge-Kutta discontinuous Galerkin (RKDG) scheme subsequently allows for an accurate and efficient representation of the tsunami evolution and inundation at the coast. This workflow allows for evaluation of how the rupture behavior affects the hydrodynamic wave propagation and coastal inundation. We present coupled results for differing earthquake scenarios. Examples include megathrust only ruptures versus ruptures with splay fault branching off the megathrust near the surface. Coupling to the tsunami simulation component is performed either dynamically (time dependent) or statically, resulting in differing tsunami wave and inundation behavior. The simplified topographical setup allows for systematic parameter studies and reproducible physical studies.

Commercial Building Energy Saver, API

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

2015-08-27

The CBES API provides Application Programming Interface to a suite of functions to improve energy efficiency of buildings, including building energy benchmarking, preliminary retrofit analysis using a pre-simulation database DEEP, and detailed retrofit analysis using energy modeling with the EnergyPlus simulation engine. The CBES API is used to power the LBNL CBES Web App. It can be adopted by third party developers and vendors into their software tools and platforms.

Multi-Constituent Simulation of Thrombus Deposition

NASA Astrophysics Data System (ADS)

Wu, Wei-Tao; Jamiolkowski, Megan A.; Wagner, William R.; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

2017-02-01

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices.

Multi-Constituent Simulation of Thrombus Deposition

PubMed Central

Wu, Wei-Tao; Jamiolkowski, Megan A.; Wagner, William R.; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

2017-01-01

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices. PMID:28218279

Multi-Constituent Simulation of Thrombus Deposition.

PubMed

Wu, Wei-Tao; Jamiolkowski, Megan A; Wagner, William R; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F

2017-02-20

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices.

Benchmarking hydrological model predictive capability for UK River flows and flood peaks.

NASA Astrophysics Data System (ADS)

Lane, Rosanna; Coxon, Gemma; Freer, Jim; Wagener, Thorsten

2017-04-01

Data and hydrological models are now available for national hydrological analyses. However, hydrological model performance varies between catchments, and lumped, conceptual models are not able to produce adequate simulations everywhere. This study aims to benchmark hydrological model performance for catchments across the United Kingdom within an uncertainty analysis framework. We have applied four hydrological models from the FUSE framework to 1128 catchments across the UK. These models are all lumped models and run at a daily timestep, but differ in the model structural architecture and process parameterisations, therefore producing different but equally plausible simulations. We apply FUSE over a 20 year period from 1988-2008, within a GLUE Monte Carlo uncertainty analyses framework. Model performance was evaluated for each catchment, model structure and parameter set using standard performance metrics. These were calculated both for the whole time series and to assess seasonal differences in model performance. The GLUE uncertainty analysis framework was then applied to produce simulated 5th and 95th percentile uncertainty bounds for the daily flow time-series and additionally the annual maximum prediction bounds for each catchment. The results show that the model performance varies significantly in space and time depending on catchment characteristics including climate, geology and human impact. We identify regions where models are systematically failing to produce good results, and present reasons why this could be the case. We also identify regions or catchment characteristics where one model performs better than others, and have explored what structural component or parameterisation enables certain models to produce better simulations in these catchments. Model predictive capability was assessed for each catchment, through looking at the ability of the models to produce discharge prediction bounds which successfully bound the observed discharge. These results improve our understanding of the predictive capability of simple conceptual hydrological models across the UK and help us to identify where further effort is needed to develop modelling approaches to better represent different catchment and climate typologies.

Validation of pore network simulations of ex-situ water distributions in a gas diffusion layer of proton exchange membrane fuel cells with X-ray tomographic images

NASA Astrophysics Data System (ADS)

Agaesse, Tristan; Lamibrac, Adrien; Büchi, Felix N.; Pauchet, Joel; Prat, Marc

2016-11-01

Understanding and modeling two-phase flows in the gas diffusion layer (GDL) of proton exchange membrane fuel cells are important in order to improve fuel cells performance. They are scientifically challenging because of the peculiarities of GDLs microstructures. In the present work, simulations on a pore network model are compared to X-ray tomographic images of water distributions during an ex-situ water invasion experiment. A method based on watershed segmentation was developed to extract a pore network from the 3D segmented image of the dry GDL. Pore network modeling and a full morphology model were then used to perform two-phase simulations and compared to the experimental data. The results show good agreement between experimental and simulated microscopic water distributions. Pore network extraction parameters were also benchmarked using the experimental data and results from full morphology simulations.

A fast elitism Gaussian estimation of distribution algorithm and application for PID optimization.

PubMed

Xu, Qingyang; Zhang, Chengjin; Zhang, Li

2014-01-01

Estimation of distribution algorithm (EDA) is an intelligent optimization algorithm based on the probability statistics theory. A fast elitism Gaussian estimation of distribution algorithm (FEGEDA) is proposed in this paper. The Gaussian probability model is used to model the solution distribution. The parameters of Gaussian come from the statistical information of the best individuals by fast learning rule. A fast learning rule is used to enhance the efficiency of the algorithm, and an elitism strategy is used to maintain the convergent performance. The performances of the algorithm are examined based upon several benchmarks. In the simulations, a one-dimensional benchmark is used to visualize the optimization process and probability model learning process during the evolution, and several two-dimensional and higher dimensional benchmarks are used to testify the performance of FEGEDA. The experimental results indicate the capability of FEGEDA, especially in the higher dimensional problems, and the FEGEDA exhibits a better performance than some other algorithms and EDAs. Finally, FEGEDA is used in PID controller optimization of PMSM and compared with the classical-PID and GA.

A Fast Elitism Gaussian Estimation of Distribution Algorithm and Application for PID Optimization

PubMed Central

Xu, Qingyang; Zhang, Chengjin; Zhang, Li

2014-01-01

Estimation of distribution algorithm (EDA) is an intelligent optimization algorithm based on the probability statistics theory. A fast elitism Gaussian estimation of distribution algorithm (FEGEDA) is proposed in this paper. The Gaussian probability model is used to model the solution distribution. The parameters of Gaussian come from the statistical information of the best individuals by fast learning rule. A fast learning rule is used to enhance the efficiency of the algorithm, and an elitism strategy is used to maintain the convergent performance. The performances of the algorithm are examined based upon several benchmarks. In the simulations, a one-dimensional benchmark is used to visualize the optimization process and probability model learning process during the evolution, and several two-dimensional and higher dimensional benchmarks are used to testify the performance of FEGEDA. The experimental results indicate the capability of FEGEDA, especially in the higher dimensional problems, and the FEGEDA exhibits a better performance than some other algorithms and EDAs. Finally, FEGEDA is used in PID controller optimization of PMSM and compared with the classical-PID and GA. PMID:24892059

Data assimilation and prognostic whole ice sheet modelling with the variationally derived, higher order, open source, and fully parallel ice sheet model VarGlaS

NASA Astrophysics Data System (ADS)

Brinkerhoff, D. J.; Johnson, J. V.

2013-07-01

We introduce a novel, higher order, finite element ice sheet model called VarGlaS (Variational Glacier Simulator), which is built on the finite element framework FEniCS. Contrary to standard procedure in ice sheet modelling, VarGlaS formulates ice sheet motion as the minimization of an energy functional, conferring advantages such as a consistent platform for making numerical approximations, a coherent relationship between motion and heat generation, and implicit boundary treatment. VarGlaS also solves the equations of enthalpy rather than temperature, avoiding the solution of a contact problem. Rather than include a lengthy model spin-up procedure, VarGlaS possesses an automated framework for model inversion. These capabilities are brought to bear on several benchmark problems in ice sheet modelling, as well as a 500 yr simulation of the Greenland ice sheet at high resolution. VarGlaS performs well in benchmarking experiments and, given a constant climate and a 100 yr relaxation period, predicts a mass evolution of the Greenland ice sheet that matches present-day observations of mass loss. VarGlaS predicts a thinning in the interior and thickening of the margins of the ice sheet.

Revisiting the PLUMBER Experiments from a Process-Diagnostics Perspective

NASA Astrophysics Data System (ADS)

Nearing, G. S.; Ruddell, B. L.; Clark, M. P.; Nijssen, B.; Peters-Lidard, C. D.

2017-12-01

The PLUMBER benchmarking experiments [1] showed that some of the most sophisticated land models (CABLE, CH-TESSEL, COLA-SSiB, ISBA-SURFEX, JULES, Mosaic, Noah, ORCHIDEE) were outperformed - in simulations of half-hourly surface energy fluxes - by instantaneous, out-of-sample, and globally-stationary regressions with no state memory. One criticism of PLUMBER is that the benchmarking methodology was not derived formally, so that applying a similar methodology with different performance metrics can result in qualitatively different results. Another common criticism of model intercomparison projects in general is that they offer little insight into process-level deficiencies in the models, and therefore are of marginal value for helping to improve the models. We address both of these issues by proposing a formal benchmarking methodology that also yields a formal and quantitative method for process-level diagnostics. We apply this to the PLUMBER experiments to show that (1) the PLUMBER conclusions were generally correct - the models use only a fraction of the information available to them from met forcing data (<50% by our analysis), and (2) all of the land models investigated by PLUMBER have similar process-level error structures, and therefore together do not represent a meaningful sample of structural or epistemic uncertainty. We conclude by suggesting two ways to improve the experimental design of model intercomparison and/or model benchmarking studies like PLUMBER. First, PLUMBER did not report model parameter values, and it is necessary to know these values to separate parameter uncertainty from structural uncertainty. This is a first order requirement if we want to use intercomparison studies to provide feedback to model development. Second, technical documentation of land models is inadequate. Future model intercomparison projects should begin with a collaborative effort by model developers to document specific differences between model structures. This could be done in a reproducible way using a unified, process-flexible system like SUMMA [2]. [1] Best, M.J. et al. (2015) 'The plumbing of land surface models: benchmarking model performance', J. Hydrometeor. [2] Clark, M.P. et al. (2015) 'A unified approach for process-based hydrologic modeling: 1. Modeling concept', Water Resour. Res.

The rotating movement of three immiscible fluids - A benchmark problem

USGS Publications Warehouse

Bakker, M.; Oude, Essink G.H.P.; Langevin, C.D.

2004-01-01

A benchmark problem involving the rotating movement of three immiscible fluids is proposed for verifying the density-dependent flow component of groundwater flow codes. The problem consists of a two-dimensional strip in the vertical plane filled with three fluids of different densities separated by interfaces. Initially, the interfaces between the fluids make a 45??angle with the horizontal. Over time, the fluids rotate to the stable position whereby the interfaces are horizontal; all flow is caused by density differences. Two cases of the problem are presented, one resulting in a symmetric flow field and one resulting in an asymmetric flow field. An exact analytical solution for the initial flow field is presented by application of the vortex theory and complex variables. Numerical results are obtained using three variable-density groundwater flow codes (SWI, MOCDENS3D, and SEAWAT). Initial horizontal velocities of the interfaces, as simulated by the three codes, compare well with the exact solution. The three codes are used to simulate the positions of the interfaces at two times; the three codes produce nearly identical results. The agreement between the results is evidence that the specific rotational behavior predicted by the models is correct. It also shows that the proposed problem may be used to benchmark variable-density codes. It is concluded that the three models can be used to model accurately the movement of interfaces between immiscible fluids, and have little or no numerical dispersion. ?? 2003 Elsevier B.V. All rights reserved.

Summary of comparison and analysis of results from exercises 1 and 2 of the OECD PBMR coupled neutronics/thermal hydraulics transient benchmark

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mkhabela, P.; Han, J.; Tyobeka, B.

2006-07-01

The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has accepted, through the Nuclear Science Committee (NSC), the inclusion of the Pebble-Bed Modular Reactor 400 MW design (PBMR-400) coupled neutronics/thermal hydraulics transient benchmark problem as part of their official activities. The scope of the benchmark is to establish a well-defined problem, based on a common given library of cross sections, to compare methods and tools in core simulation and thermal hydraulics analysis with a specific focus on transient events through a set of multi-dimensional computational test problems. The benchmark includes three steady state exercises andmore » six transient exercises. This paper describes the first two steady state exercises, their objectives and the international participation in terms of organization, country and computer code utilized. This description is followed by a comparison and analysis of the participants' results submitted for these two exercises. The comparison of results from different codes allows for an assessment of the sensitivity of a result to the method employed and can thus help to focus the development efforts on the most critical areas. The two first exercises also allow for removing of user-related modeling errors and prepare core neutronics and thermal-hydraulics models of the different codes for the rest of the exercises in the benchmark. (authors)« less

Consideration of Real World Factors Influencing Greenhouse Gas Emissions in ALPHA

EPA Science Inventory

Discuss a variety of factors that influence the simulated fuel economy and GHG emissions that are often overlooked and updates made to ALPHA based on actual benchmarking data observed across a range of vehicles and transmissions. ALPHA model calibration is also examined, focusin...

Control strategies for nitrous oxide emissions reduction on wastewater treatment plants operation.

PubMed

Santín, I; Barbu, M; Pedret, C; Vilanova, R

2017-11-15

The present paper focused on reducing greenhouse gases emissions in wastewater treatment plants operation by application of suitable control strategies. Specifically, the objective is to reduce nitrous oxide emissions during the nitrification process. Incomplete nitrification in the aerobic tanks can lead to an accumulation of nitrite that triggers the nitrous oxide emissions. In order to avoid the peaks of nitrous oxide emissions, this paper proposes a cascade control configuration by manipulating the dissolved oxygen set-points in the aerobic tanks. This control strategy is combined with ammonia cascade control already applied in the literature. This is performed with the objective to take also into account effluent pollutants and operational costs. In addition, other greenhouse gases emissions sources are also evaluated. Results have been obtained by simulation, using a modified version of Benchmark Simulation Model no. 2, which takes into account greenhouse gases emissions. This is called Benchmark Simulation Model no. 2 Gas. The results show that the proposed control strategies are able to reduce by 29.86% of nitrous oxide emissions compared to the default control strategy, while maintaining a satisfactory trade-off between water quality and costs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas

2009-01-01

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors,more » other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million atom biological systems scale well up to 30k cores, producing 30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.« less

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

PubMed

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C

2009-10-13

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to ∼30k cores, producing ∼30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.

A versatile model for soft patchy particles with various patch arrangements.

PubMed

Li, Zhan-Wei; Zhu, You-Liang; Lu, Zhong-Yuan; Sun, Zhao-Yan

2016-01-21

We propose a simple and general mesoscale soft patchy particle model, which can felicitously describe the deformable and surface-anisotropic characteristics of soft patchy particles. This model can be used in dynamics simulations to investigate the aggregation behavior and mechanism of various types of soft patchy particles with tunable number, size, direction, and geometrical arrangement of the patches. To improve the computational efficiency of this mesoscale model in dynamics simulations, we give the simulation algorithm that fits the compute unified device architecture (CUDA) framework of NVIDIA graphics processing units (GPUs). The validation of the model and the performance of the simulations using GPUs are demonstrated by simulating several benchmark systems of soft patchy particles with 1 to 4 patches in a regular geometrical arrangement. Because of its simplicity and computational efficiency, the soft patchy particle model will provide a powerful tool to investigate the aggregation behavior of soft patchy particles, such as patchy micelles, patchy microgels, and patchy dendrimers, over larger spatial and temporal scales.

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

PubMed

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

Community-based benchmarking of the CMIP DECK experiments

NASA Astrophysics Data System (ADS)

Gleckler, P. J.

2015-12-01

A diversity of community-based efforts are independently developing "diagnostic packages" with little or no coordination between them. A short list of examples include NCAR's Climate Variability Diagnostics Package (CVDP), ORNL's International Land Model Benchmarking (ILAMB), LBNL's Toolkit for Extreme Climate Analysis (TECA), PCMDI's Metrics Package (PMP), the EU EMBRACE ESMValTool, the WGNE MJO diagnostics package, and CFMIP diagnostics. The full value of these efforts cannot be realized without some coordination. As a first step, a WCRP effort has initiated a catalog to document candidate packages that could potentially be applied in a "repeat-use" fashion to all simulations contributed to the CMIP DECK (Diagnostic, Evaluation and Characterization of Klima) experiments. Some coordination of community-based diagnostics has the additional potential to improve how CMIP modeling groups analyze their simulations during model-development. The fact that most modeling groups now maintain a "CMIP compliant" data stream means that in principal without much effort they could readily adopt a set of well organized diagnostic capabilities specifically designed to operate on CMIP DECK experiments. Ultimately, a detailed listing of and access to analysis codes that are demonstrated to work "out of the box" with CMIP data could enable model developers (and others) to select those codes they wish to implement in-house, potentially enabling more systematic evaluation during the model development process.

Using in-situ observations of atmospheric water vapor isotopes to benchmark and isotope-enabled General Circulation Models and improve ice core paleo-climate reconstruction

NASA Astrophysics Data System (ADS)

Steen-Larsen, Hans Christian; Sveinbjörnsdottir, Arny; Masson-Delmotte, Valerie; Werner, Martin; Risi, Camille; Yoshimura, Kei

2016-04-01

We have since 2010 carried out in-situ continuous water vapor isotope observations on top of the Greenland Ice Sheet (3 seasons at NEEM), in Svalbard (1 year), in Iceland (4 years), in Bermuda (4 years). The expansive dataset containing high accuracy and precision measurements of δ18O, δD, and the d-excess allow us to validate and benchmark the treatment of the atmospheric hydrological cycle's processes in General Circulation Models using simulations nudged to reanalysis products. Recent findings from both Antarctica and Greenland have documented strong interaction between the snow surface isotopes and the near surface atmospheric water vapor isotopes on diurnal to synoptic time scales. In fact, it has been shown that the snow surface isotopes take up the synoptic driven atmospheric water vapor isotopic signal in-between precipitation events, erasing the precipitation isotope signal in the surface snow. This highlights the importance of using General or Regional Climate Models, which accurately are able to simulate the atmospheric water vapor isotopic composition, to understand and interpret the ice core isotope signal. With this in mind we have used three isotope-enabled General Circulation Models (isoGSM, ECHAM5-wiso, and LMDZiso) nudged to reanalysis products. We have compared the simulations of daily mean isotope values directly with our in-situ observations. This has allowed us to characterize the variability of the isotopic composition in the models and compared it to our observations. We have specifically focused on the d-excess in order to characterize why both the mean and the variability is significantly lower than our observations. We argue that using water vapor isotopes to benchmark General Circulation Models offers an excellent tool for improving the treatment and parameterization of the atmospheric hydrological cycle. Recent studies have documented a very large inter-model dispersion in the treatment of the Arctic water cycle under a future global warming and greenhouse gas emission scenario. Our results call for action to create an international pan-Arctic monitoring water vapor isotope network in order to improve future projections of Arctic climate.

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Simulation Studies for Inspection of the Benchmark Test with PATRASH

NASA Astrophysics Data System (ADS)

Shimosaki, Y.; Igarashi, S.; Machida, S.; Shirakata, M.; Takayama, K.; Noda, F.; Shigaki, K.

2002-12-01

In order to delineate the halo-formation mechanisms in a typical FODO lattice, a 2-D simulation code PATRASH (PArticle TRAcking in a Synchrotron for Halo analysis) has been developed. The electric field originating from the space charge is calculated by the Hybrid Tree code method. Benchmark tests utilizing three simulation codes of ACCSIM, PATRASH and SIMPSONS were carried out. These results have been confirmed to be fairly in agreement with each other. The details of PATRASH simulation are discussed with some examples.

MEqTrees Telescope and Radio-sky Simulations and CPU Benchmarking

NASA Astrophysics Data System (ADS)

Shanmugha Sundaram, G. A.

2009-09-01

MEqTrees is a Python-based implementation of the classical Measurement Equation, wherein the various 2×2 Jones matrices are parametrized representations in the spatial and sky domains for any generic radio telescope. Customized simulations of radio-source sky models and corrupt Jones terms are demonstrated based on a policy framework, with performance estimates derived for array configurations, ``dirty''-map residuals and processing power requirements for such computations on conventional platforms.

Dimethyl methylphosphonate adsorption and decomposition on MoO2 as studied by ambient pressure x-ray photoelectron spectroscopy and DFT calculations

NASA Astrophysics Data System (ADS)

Head, Ashley R.; Tsyshevsky, Roman; Trotochaud, Lena; Yu, Yi; Karslıoǧlu, Osman; Eichhorn, Bryan; Kuklja, Maija M.; Bluhm, Hendrik

2018-04-01

Organophosphonates range in their toxicity and are used as pesticides, herbicides, and chemical warfare agents (CWAs). Few laboratories are equipped to handle the most toxic molecules, thus simulants such as dimethyl methylphosphonate (DMMP), are used as a first step in studying adsorption and reactivity on materials. Benchmarked by combined experimental and theoretical studies of simulants, calculations offer an opportunity to understand how molecular interactions with a surface changes upon using a CWA. However, most calculations of DMMP and CWAs on surfaces are limited to adsorption studies on clusters of atoms, which may differ markedly from the behavior on bulk solid-state materials with extended surfaces. We have benchmarked our solid-state periodic calculations of DMMP adsorption and reactivity on MoO2 with ambient pressure x-ray photoelectron spectroscopy studies (APXPS). DMMP is found to interact strongly with a MoO2 film, a model system for the MoO x component in the ASZM-TEDA© gas filtration material. Density functional theory modeling of several adsorption and decomposition mechanisms assist the assignment of APXPS peaks. Our results show that some of the adsorbed DMMP decomposes, with all the products remaining on the surface. The rigorous calculations benchmarked with experiments pave a path to reliable and predictive theoretical studies of CWA interactions with surfaces.

Simulation of the pulse propagation by the interacting mode parabolic equation method

NASA Astrophysics Data System (ADS)

Trofimov, M. Yu.; Kozitskiy, S. B.; Zakharenko, A. D.

2018-07-01

A broadband modeling of pulses has been performed by using the previously derived interacting mode parabolic equation through the Fourier synthesis. Test examples on the wedge with the angle 2.86∘ (known as the ASA benchmark) show excellent agreement with the source images method.

Commercial Building Energy Saver, Web App

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

The CBES App is a web-based toolkit for use by small businesses and building owners and operators of small and medium size commercial buildings to perform energy benchmarking and retrofit analysis for buildings. The CBES App analyzes the energy performance of user's building for pre-and posto-retrofit, in conjunction with user's input data, to identify recommended retrofit measures, energy savings and economic analysis for the selected measures. The CBES App provides energy benchmarking, including getting an EnergyStar score using EnergyStar API and benchmarking against California peer buildings using the EnergyIQ API. The retrofit analysis includes a preliminary analysis by looking upmore » retrofit measures from a pre-simulated database DEEP, and a detailed analysis creating and running EnergyPlus models to calculate energy savings of retrofit measures. The CBES App builds upon the LBNL CBES API.« less

Benchmarking study of the MCNP code against cold critical experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitaraman, S.

1991-01-01

The purpose of this study was to benchmark the widely used Monte Carlo code MCNP against a set of cold critical experiments with a view to using the code as a means of independently verifying the performance of faster but less accurate Monte Carlo and deterministic codes. The experiments simulated consisted of both fast and thermal criticals as well as fuel in a variety of chemical forms. A standard set of benchmark cold critical experiments was modeled. These included the two fast experiments, GODIVA and JEZEBEL, the TRX metallic uranium thermal experiments, the Babcock and Wilcox oxide and mixed oxidemore » experiments, and the Oak Ridge National Laboratory (ORNL) and Pacific Northwest Laboratory (PNL) nitrate solution experiments. The principal case studied was a small critical experiment that was performed with boiling water reactor bundles.« less

Creation of problem-dependent Doppler-broadened cross sections in the KENO Monte Carlo code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, Shane W. D.; Celik, Cihangir; Maldonado, G. Ivan

2015-11-06

In this paper, we introduce a quick method for improving the accuracy of Monte Carlo simulations by generating one- and two-dimensional cross sections at a user-defined temperature before performing transport calculations. A finite difference method is used to Doppler-broaden cross sections to the desired temperature, and unit-base interpolation is done to generate the probability distributions for double differential two-dimensional thermal moderator cross sections at any arbitrarily user-defined temperature. The accuracy of these methods is tested using a variety of contrived problems. In addition, various benchmarks at elevated temperatures are modeled, and results are compared with benchmark results. Lastly, the problem-dependentmore » cross sections are observed to produce eigenvalue estimates that are closer to the benchmark results than those without the problem-dependent cross sections.« less

Performance Evaluation and Improvement of Ferroelectric Field-Effect Transistor Memory

NASA Astrophysics Data System (ADS)

Yu, Hyung Suk

Flash memory is reaching scaling limitations rapidly due to reduction of charge in floating gates, charge leakage and capacitive coupling between cells which cause threshold voltage fluctuations, short retention times, and interference. Many new memory technologies are being considered as alternatives to flash memory in an effort to overcome these limitations. Ferroelectric Field-Effect Transistor (FeFET) is one of the main emerging candidates because of its structural similarity to conventional FETs and fast switching speed. Nevertheless, the performance of FeFETs have not been systematically compared and analyzed against other competing technologies. In this work, we first benchmark the intrinsic performance of FeFETs and other memories by simulations in order to identify the strengths and weaknesses of FeFETs. To simulate realistic memory applications, we compare memories on an array structure. For the comparisons, we construct an accurate delay model and verify it by benchmarking against exact HSPICE simulations. Second, we propose an accurate model for FeFET memory window since the existing model has limitations. The existing model assumes symmetric operation voltages but it is not valid for the practical asymmetric operation voltages. In this modeling, we consider practical operation voltages and device dimensions. Also, we investigate realistic changes of memory window over time and retention time of FeFETs. Last, to improve memory window and subthreshold swing, we suggest nonplanar junctionless structures for FeFETs. Using the suggested structures, we study the dimensional dependences of crucial parameters like memory window and subthreshold swing and also analyze key interference mechanisms.

Simulation-based comprehensive benchmarking of RNA-seq aligners

PubMed Central

Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; Di Camillo, Barbara; FitzGerald, Garret A; Grant, Gregory R

2018-01-01

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings. PMID:27941783

Uncertainty and sensitivity analysis of control strategies using the benchmark simulation model No1 (BSM1).

PubMed

Flores-Alsina, Xavier; Rodriguez-Roda, Ignasi; Sin, Gürkan; Gernaey, Krist V

2009-01-01

The objective of this paper is to perform an uncertainty and sensitivity analysis of the predictions of the Benchmark Simulation Model (BSM) No. 1, when comparing four activated sludge control strategies. The Monte Carlo simulation technique is used to evaluate the uncertainty in the BSM1 predictions, considering the ASM1 bio-kinetic parameters and influent fractions as input uncertainties while the Effluent Quality Index (EQI) and the Operating Cost Index (OCI) are focused on as model outputs. The resulting Monte Carlo simulations are presented using descriptive statistics indicating the degree of uncertainty in the predicted EQI and OCI. Next, the Standard Regression Coefficients (SRC) method is used for sensitivity analysis to identify which input parameters influence the uncertainty in the EQI predictions the most. The results show that control strategies including an ammonium (S(NH)) controller reduce uncertainty in both overall pollution removal and effluent total Kjeldahl nitrogen. Also, control strategies with an external carbon source reduce the effluent nitrate (S(NO)) uncertainty increasing both their economical cost and variability as a trade-off. Finally, the maximum specific autotrophic growth rate (micro(A)) causes most of the variance in the effluent for all the evaluated control strategies. The influence of denitrification related parameters, e.g. eta(g) (anoxic growth rate correction factor) and eta(h) (anoxic hydrolysis rate correction factor), becomes less important when a S(NO) controller manipulating an external carbon source addition is implemented.

Modeling spatial-temporal dynamics of global wetlands: Comprehensive evaluation of a new sub-grid TOPMODEL parameterization and uncertainties

NASA Astrophysics Data System (ADS)

Zhang, Z.; Zimmermann, N. E.; Poulter, B.

2015-12-01

Simulations of the spatial-temporal dynamics of wetlands is key to understanding the role of wetland biogeochemistry under past and future climate variability. Hydrologic inundation models, such as TOPMODEL, are based on a fundamental parameter known as the compound topographic index (CTI) and provide a computationally cost-efficient approach to simulate global wetland dynamics. However, there remains large discrepancy in the implementations of TOPMODEL in land-surface models (LSMs) and thus their performance against observations. This study describes new improvements to TOPMODEL implementation and estimates of global wetland dynamics using the LPJ-wsl DGVM, and quantifies uncertainties by comparing three digital elevation model products (HYDRO1k, GMTED, and HydroSHEDS) at different spatial resolution and accuracy on simulated inundation dynamics. We found that calibrating TOPMODEL with a benchmark dataset can help to successfully predict the seasonal and interannual variations of wetlands, as well as improve the spatial distribution of wetlands to be consistent with inventories. The HydroSHEDS DEM, using a river-basin scheme for aggregating the CTI, shows best accuracy for capturing the spatio-temporal dynamics of wetland among three DEM products. This study demonstrates the feasibility to capture spatial heterogeneity of inundation and to estimate seasonal and interannual variations in wetland by coupling a hydrological module in LSMs with appropriate benchmark datasets. It additionally highlight the importance of an adequate understanding of topographic indices for simulating global wetlands and show the opportunity to converge wetland estimations in LSMs by identifying the uncertainty associated with existing wetland products.

Three-dimensional benchmark for variable-density flow and transport simulation: matching semi-analytic stability modes for steady unstable convection in an inclined porous box

USGS Publications Warehouse

Voss, Clifford I.; Simmons, Craig T.; Robinson, Neville I.

2010-01-01

This benchmark for three-dimensional (3D) numerical simulators of variable-density groundwater flow and solute or energy transport consists of matching simulation results with the semi-analytical solution for the transition from one steady-state convective mode to another in a porous box. Previous experimental and analytical studies of natural convective flow in an inclined porous layer have shown that there are a variety of convective modes possible depending on system parameters, geometry and inclination. In particular, there is a well-defined transition from the helicoidal mode consisting of downslope longitudinal rolls superimposed upon an upslope unicellular roll to a mode consisting of purely an upslope unicellular roll. Three-dimensional benchmarks for variable-density simulators are currently (2009) lacking and comparison of simulation results with this transition locus provides an unambiguous means to test the ability of such simulators to represent steady-state unstable 3D variable-density physics.

A Simulation Environment for Benchmarking Sensor Fusion-Based Pose Estimators.

PubMed

Ligorio, Gabriele; Sabatini, Angelo Maria

2015-12-19

In-depth analysis and performance evaluation of sensor fusion-based estimators may be critical when performed using real-world sensor data. For this reason, simulation is widely recognized as one of the most powerful tools for algorithm benchmarking. In this paper, we present a simulation framework suitable for assessing the performance of sensor fusion-based pose estimators. The systems used for implementing the framework were magnetic/inertial measurement units (MIMUs) and a camera, although the addition of further sensing modalities is straightforward. Typical nuisance factors were also included for each sensor. The proposed simulation environment was validated using real-life sensor data employed for motion tracking. The higher mismatch between real and simulated sensors was about 5% of the measured quantity (for the camera simulation), whereas a lower correlation was found for an axis of the gyroscope (0.90). In addition, a real benchmarking example of an extended Kalman filter for pose estimation from MIMU and camera data is presented.

Continuity-based model interfacing for plant-wide simulation: a general approach.

PubMed

Volcke, Eveline I P; van Loosdrecht, Mark C M; Vanrolleghem, Peter A

2006-08-01

In plant-wide simulation studies of wastewater treatment facilities, often existing models from different origin need to be coupled. However, as these submodels are likely to contain different state variables, their coupling is not straightforward. The continuity-based interfacing method (CBIM) provides a general framework to construct model interfaces for models of wastewater systems, taking into account conservation principles. In this contribution, the CBIM approach is applied to study the effect of sludge digestion reject water treatment with a SHARON-Anammox process on a plant-wide scale. Separate models were available for the SHARON process and for the Anammox process. The Benchmark simulation model no. 2 (BSM2) is used to simulate the behaviour of the complete WWTP including sludge digestion. The CBIM approach is followed to develop three different model interfaces. At the same time, the generally applicable CBIM approach was further refined and particular issues when coupling models in which pH is considered as a state variable, are pointed out.

LES-based filter-matrix lattice Boltzmann model for simulating fully developed turbulent channel flow

NASA Astrophysics Data System (ADS)

Zhuo, Congshan; Zhong, Chengwen

2016-11-01

In this paper, a three-dimensional filter-matrix lattice Boltzmann (FMLB) model based on large eddy simulation (LES) was verified for simulating wall-bounded turbulent flows. The Vreman subgrid-scale model was employed in the present FMLB-LES framework, which had been proved to be capable of predicting turbulent near-wall region accurately. The fully developed turbulent channel flows were performed at a friction Reynolds number Reτ of 180. The turbulence statistics computed from the present FMLB-LES simulations, including mean stream velocity profile, Reynolds stress profile and root-mean-square velocity fluctuations greed well with the LES results of multiple-relaxation-time (MRT) LB model, and some discrepancies in comparison with those direct numerical simulation (DNS) data of Kim et al. was also observed due to the relatively low grid resolution. Moreover, to investigate the influence of grid resolution on the present LES simulation, a DNS simulation on a finer gird was also implemented by present FMLB-D3Q19 model. Comparisons of detailed computed various turbulence statistics with available benchmark data of DNS showed quite well agreement.

Finite-element modelling of physics-based hillslope hydrology, Keith Beven, and beyond

USGS Publications Warehouse

Loague, Keith; Ebel, Brian A.

2016-01-01

Keith Beven is a voice of reason on the intelligent use of models and the subsequent acknowledgement/assessment of the uncertainties associated with environmental simula-tion. With several books and hundreds of papers, Keith’s work is widespread, well known, and highly referenced. Four of Keith’s most notable contributions are the iconic TOPMODEL (Beven and Kirkby, 1979), classic papers on macropores and preferential flow (Beven and Germann, 1982, 2013), two editions of the rainfall-runoff modelling bible (Beven, 2000a, 2012), and the selection/commentary for the first volume from the Benchmark Papers in Hydrology series (Beven, 2006b). Remarkably, the thirty-one papers in his benchmark volume, entitled Streamflow Generation Processes, are not tales of modelling wizardry but describe measurements designed to better understand the dynamics of near-surface systems (quintessential Keith). The impetus for this commentary is Keith’sPhD research (Beven, 1975), where he developed a new finite-element model and conducted concept-development simu-lations based upon the processes identified by, for example, Richards (1931), Horton (1933), Hubbert (1940), Hewlett and Hibbert (1963), and Dunne and Black (1970a,b). Readers not familiar with the different mechanisms of streamflow generation are referred to Dunne (1978).

Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture

PubMed Central

Knight, James C.; Furber, Steve B.

2016-01-01

While the adult human brain has approximately 8.8 × 1010 neurons, this number is dwarfed by its 1 × 1015 synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously. PMID:27683540

The NAS kernel benchmark program

NASA Technical Reports Server (NTRS)

Bailey, D. H.; Barton, J. T.

1985-01-01

A collection of benchmark test kernels that measure supercomputer performance has been developed for the use of the NAS (Numerical Aerodynamic Simulation) program at the NASA Ames Research Center. This benchmark program is described in detail and the specific ground rules are given for running the program as a performance test.

An MPI-based MoSST core dynamics model

NASA Astrophysics Data System (ADS)

Jiang, Weiyuan; Kuang, Weijia

2008-09-01

Distributed systems are among the main cost-effective and expandable platforms for high-end scientific computing. Therefore scalable numerical models are important for effective use of such systems. In this paper, we present an MPI-based numerical core dynamics model for simulation of geodynamo and planetary dynamos, and for simulation of core-mantle interactions. The model is developed based on MPI libraries. Two algorithms are used for node-node communication: a "master-slave" architecture and a "divide-and-conquer" architecture. The former is easy to implement but not scalable in communication. The latter is scalable in both computation and communication. The model scalability is tested on Linux PC clusters with up to 128 nodes. This model is also benchmarked with a published numerical dynamo model solution.

Bio-inspired benchmark generator for extracellular multi-unit recordings

PubMed Central

Mondragón-González, Sirenia Lizbeth; Burguière, Eric

2017-01-01

The analysis of multi-unit extracellular recordings of brain activity has led to the development of numerous tools, ranging from signal processing algorithms to electronic devices and applications. Currently, the evaluation and optimisation of these tools are hampered by the lack of ground-truth databases of neural signals. These databases must be parameterisable, easy to generate and bio-inspired, i.e. containing features encountered in real electrophysiological recording sessions. Towards that end, this article introduces an original computational approach to create fully annotated and parameterised benchmark datasets, generated from the summation of three components: neural signals from compartmental models and recorded extracellular spikes, non-stationary slow oscillations, and a variety of different types of artefacts. We present three application examples. (1) We reproduced in-vivo extracellular hippocampal multi-unit recordings from either tetrode or polytrode designs. (2) We simulated recordings in two different experimental conditions: anaesthetised and awake subjects. (3) Last, we also conducted a series of simulations to study the impact of different level of artefacts on extracellular recordings and their influence in the frequency domain. Beyond the results presented here, such a benchmark dataset generator has many applications such as calibration, evaluation and development of both hardware and software architectures. PMID:28233819

Efficient Modeling of Laser-Plasma Accelerators with INF&RNO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benedetti, C.; Schroeder, C. B.; Esarey, E.

2010-06-01

The numerical modeling code INF&RNO (INtegrated Fluid& paRticle simulatioN cOde, pronounced"inferno") is presented. INF&RNO is an efficient 2D cylindrical code to model the interaction of a short laser pulse with an underdense plasma. The code is based on an envelope model for the laser while either a PIC or a fluid description can be used for the plasma. The effect of the laser pulse on the plasma is modeled with the time-averaged poderomotive force. These and other features allow for a speedup of 2-4 orders of magnitude compared to standard full PIC simulations while still retaining physical fidelity. The codemore » has been benchmarked against analytical solutions and 3D PIC simulations and here a set of validation tests together with a discussion of the performances are presented.« less

Efficient Modeling of Laser-Plasma Accelerators with INF&RNO

NASA Astrophysics Data System (ADS)

Benedetti, C.; Schroeder, C. B.; Esarey, E.; Geddes, C. G. R.; Leemans, W. P.

2010-11-01

The numerical modeling code INF&RNO (INtegrated Fluid & paRticle simulatioN cOde, pronounced "inferno") is presented. INF&RNO is an efficient 2D cylindrical code to model the interaction of a short laser pulse with an underdense plasma. The code is based on an envelope model for the laser while either a PIC or a fluid description can be used for the plasma. The effect of the laser pulse on the plasma is modeled with the time-averaged poderomotive force. These and other features allow for a speedup of 2-4 orders of magnitude compared to standard full PIC simulations while still retaining physical fidelity. The code has been benchmarked against analytical solutions and 3D PIC simulations and here a set of validation tests together with a discussion of the performances are presented.

Simulation of networks of spiking neurons: A review of tools and strategies

PubMed Central

Brette, Romain; Rudolph, Michelle; Carnevale, Ted; Hines, Michael; Beeman, David; Bower, James M.; Diesmann, Markus; Morrison, Abigail; Goodman, Philip H.; Harris, Frederick C.; Zirpe, Milind; Natschläger, Thomas; Pecevski, Dejan; Ermentrout, Bard; Djurfeldt, Mikael; Lansner, Anders; Rochel, Olivier; Vieville, Thierry; Muller, Eilif; Davison, Andrew P.; El Boustani, Sami

2009-01-01

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin–Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks. PMID:17629781

Modeling spatial-temporal dynamics of global wetlands: comprehensive evaluation of a new sub-grid TOPMODEL parameterization and uncertainties

NASA Astrophysics Data System (ADS)

Zhang, Z.; Zimmermann, N. E.; Poulter, B.

2015-11-01

Simulations of the spatial-temporal dynamics of wetlands are key to understanding the role of wetland biogeochemistry under past and future climate variability. Hydrologic inundation models, such as TOPMODEL, are based on a fundamental parameter known as the compound topographic index (CTI) and provide a computationally cost-efficient approach to simulate wetland dynamics at global scales. However, there remains large discrepancy in the implementations of TOPMODEL in land-surface models (LSMs) and thus their performance against observations. This study describes new improvements to TOPMODEL implementation and estimates of global wetland dynamics using the LPJ-wsl dynamic global vegetation model (DGVM), and quantifies uncertainties by comparing three digital elevation model products (HYDRO1k, GMTED, and HydroSHEDS) at different spatial resolution and accuracy on simulated inundation dynamics. In addition, we found that calibrating TOPMODEL with a benchmark wetland dataset can help to successfully delineate the seasonal and interannual variations of wetlands, as well as improve the spatial distribution of wetlands to be consistent with inventories. The HydroSHEDS DEM, using a river-basin scheme for aggregating the CTI, shows best accuracy for capturing the spatio-temporal dynamics of wetlands among the three DEM products. The estimate of global wetland potential/maximum is ∼ 10.3 Mkm2 (106 km2), with a mean annual maximum of ∼ 5.17 Mkm2 for 1980-2010. This study demonstrates the feasibility to capture spatial heterogeneity of inundation and to estimate seasonal and interannual variations in wetland by coupling a hydrological module in LSMs with appropriate benchmark datasets. It additionally highlights the importance of an adequate investigation of topographic indices for simulating global wetlands and shows the opportunity to converge wetland estimates across LSMs by identifying the uncertainty associated with existing wetland products.

Binary Associative Memories as a Benchmark for Spiking Neuromorphic Hardware

PubMed Central

Stöckel, Andreas; Jenzen, Christoph; Thies, Michael; Rückert, Ulrich

2017-01-01

Large-scale neuromorphic hardware platforms, specialized computer systems for energy efficient simulation of spiking neural networks, are being developed around the world, for example as part of the European Human Brain Project (HBP). Due to conceptual differences, a universal performance analysis of these systems in terms of runtime, accuracy and energy efficiency is non-trivial, yet indispensable for further hard- and software development. In this paper we describe a scalable benchmark based on a spiking neural network implementation of the binary neural associative memory. We treat neuromorphic hardware and software simulators as black-boxes and execute exactly the same network description across all devices. Experiments on the HBP platforms under varying configurations of the associative memory show that the presented method allows to test the quality of the neuron model implementation, and to explain significant deviations from the expected reference output. PMID:28878642

A partial entropic lattice Boltzmann MHD simulation of the Orszag-Tang vortex

NASA Astrophysics Data System (ADS)

Flint, Christopher; Vahala, George

2018-02-01

Karlin has introduced an analytically determined entropic lattice Boltzmann (LB) algorithm for Navier-Stokes turbulence. Here, this is partially extended to an LB model of magnetohydrodynamics, on using the vector distribution function approach of Dellar for the magnetic field (which is permitted to have field reversal). The partial entropic algorithm is benchmarked successfully against standard simulations of the Orszag-Tang vortex [Orszag, S.A.; Tang, C.M. J. Fluid Mech. 1979, 90 (1), 129-143].

MCNP modelling of scintillation-detector gamma-ray spectra from natural radionuclides.

PubMed

Hendriks, P H G M; Maucec, M; de Meijer, R J

2002-09-01

gamma-ray spectra of natural radionuclides are simulated for a BGO detector in a borehole geometry using the Monte Carlo code MCNP. All gamma-ray emissions of the decay of 40K and the series of 232Th and 238U are used to describe the source. A procedure is proposed which excludes the time-consuming electron tracking in less relevant areas of the geometry. The simulated gamma-ray spectra are benchmarked against laboratory data.

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

PubMed Central

2015-01-01

We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495

Assessment of the effect of population and diary sampling methods on estimation of school-age children exposure to fine particles.

PubMed

Che, W W; Frey, H Christopher; Lau, Alexis K H

2014-12-01

Population and diary sampling methods are employed in exposure models to sample simulated individuals and their daily activity on each simulation day. Different sampling methods may lead to variations in estimated human exposure. In this study, two population sampling methods (stratified-random and random-random) and three diary sampling methods (random resampling, diversity and autocorrelation, and Markov-chain cluster [MCC]) are evaluated. Their impacts on estimated children's exposure to ambient fine particulate matter (PM2.5 ) are quantified via case studies for children in Wake County, NC for July 2002. The estimated mean daily average exposure is 12.9 μg/m(3) for simulated children using the stratified population sampling method, and 12.2 μg/m(3) using the random sampling method. These minor differences are caused by the random sampling among ages within census tracts. Among the three diary sampling methods, there are differences in the estimated number of individuals with multiple days of exposures exceeding a benchmark of concern of 25 μg/m(3) due to differences in how multiday longitudinal diaries are estimated. The MCC method is relatively more conservative. In case studies evaluated here, the MCC method led to 10% higher estimation of the number of individuals with repeated exposures exceeding the benchmark. The comparisons help to identify and contrast the capabilities of each method and to offer insight regarding implications of method choice. Exposure simulation results are robust to the two population sampling methods evaluated, and are sensitive to the choice of method for simulating longitudinal diaries, particularly when analyzing results for specific microenvironments or for exposures exceeding a benchmark of concern. © 2014 Society for Risk Analysis.

Validation of hydrogen gas stratification and mixing models

DOE PAGES

Wu, Hsingtzu; Zhao, Haihua

2015-05-26

Two validation benchmarks confirm that the BMIX++ code is capable of simulating unintended hydrogen release scenarios efficiently. The BMIX++ (UC Berkeley mechanistic MIXing code in C++) code has been developed to accurately and efficiently predict the fluid mixture distribution and heat transfer in large stratified enclosures for accident analyses and design optimizations. The BMIX++ code uses a scaling based one-dimensional method to achieve large reduction in computational effort compared to a 3-D computational fluid dynamics (CFD) simulation. Two BMIX++ benchmark models have been developed. One is for a single buoyant jet in an open space and another is for amore » large sealed enclosure with both a jet source and a vent near the floor. Both of them have been validated by comparisons with experimental data. Excellent agreements are observed. The entrainment coefficients of 0.09 and 0.08 are found to fit the experimental data for hydrogen leaks with the Froude number of 99 and 268 best, respectively. In addition, the BIX++ simulation results of the average helium concentration for an enclosure with a vent and a single jet agree with the experimental data within a margin of about 10% for jet flow rates ranging from 1.21 × 10⁻⁴ to 3.29 × 10⁻⁴ m³/s. In conclusion, computing time for each BMIX++ model with a normal desktop computer is less than 5 min.« less

Mapping the Martian Meteorology

NASA Technical Reports Server (NTRS)

Allison, Michael; Ross, J. D.; Soloman, N.

1999-01-01

The Mars-adapted version of the NASA/GISS general circulation model (GCM) has been applied to the hourly/daily simulation of the planet's meteorology over several seasonal orbits. The current running version of the model includes a diurnal solar cycle, CO2 sublimation, and a mature parameterization of upper level wave drag with a vertical domain extending from the surface up to the 6 micro b level. The benchmark simulations provide a four-dimensional archive for the comparative evaluation of various schemes for the retrieval of winds from anticipated polar orbiter measurements of temperatures by the Pressure Modulator Infrared Radiometer.

Efficient generation of connectivity in neuronal networks from simulator-independent descriptions

PubMed Central

Djurfeldt, Mikael; Davison, Andrew P.; Eppler, Jochen M.

2014-01-01

Simulator-independent descriptions of connectivity in neuronal networks promise greater ease of model sharing, improved reproducibility of simulation results, and reduced programming effort for computational neuroscientists. However, until now, enabling the use of such descriptions in a given simulator in a computationally efficient way has entailed considerable work for simulator developers, which must be repeated for each new connectivity-generating library that is developed. We have developed a generic connection generator interface that provides a standard way to connect a connectivity-generating library to a simulator, such that one library can easily be replaced by another, according to the modeler's needs. We have used the connection generator interface to connect C++ and Python implementations of the previously described connection-set algebra to the NEST simulator. We also demonstrate how the simulator-independent modeling framework PyNN can transparently take advantage of this, passing a connection description through to the simulator layer for rapid processing in C++ where a simulator supports the connection generator interface and falling-back to slower iteration in Python otherwise. A set of benchmarks demonstrates the good performance of the interface. PMID:24795620

StirMark Benchmark: audio watermarking attacks based on lossy compression

NASA Astrophysics Data System (ADS)

Steinebach, Martin; Lang, Andreas; Dittmann, Jana

2002-04-01

StirMark Benchmark is a well-known evaluation tool for watermarking robustness. Additional attacks are added to it continuously. To enable application based evaluation, in our paper we address attacks against audio watermarks based on lossy audio compression algorithms to be included in the test environment. We discuss the effect of different lossy compression algorithms like MPEG-2 audio Layer 3, Ogg or VQF on a selection of audio test data. Our focus is on changes regarding the basic characteristics of the audio data like spectrum or average power and on removal of embedded watermarks. Furthermore we compare results of different watermarking algorithms and show that lossy compression is still a challenge for most of them. There are two strategies for adding evaluation of robustness against lossy compression to StirMark Benchmark: (a) use of existing free compression algorithms (b) implementation of a generic lossy compression simulation. We discuss how such a model can be implemented based on the results of our tests. This method is less complex, as no real psycho acoustic model has to be applied. Our model can be used for audio watermarking evaluation of numerous application fields. As an example, we describe its importance for e-commerce applications with watermarking security.

The MCNP6 Analytic Criticality Benchmark Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Forrest B.

2016-06-16

Analytical benchmarks provide an invaluable tool for verifying computer codes used to simulate neutron transport. Several collections of analytical benchmark problems [1-4] are used routinely in the verification of production Monte Carlo codes such as MCNP® [5,6]. Verification of a computer code is a necessary prerequisite to the more complex validation process. The verification process confirms that a code performs its intended functions correctly. The validation process involves determining the absolute accuracy of code results vs. nature. In typical validations, results are computed for a set of benchmark experiments using a particular methodology (code, cross-section data with uncertainties, and modeling)more » and compared to the measured results from the set of benchmark experiments. The validation process determines bias, bias uncertainty, and possibly additional margins. Verification is generally performed by the code developers, while validation is generally performed by code users for a particular application space. The VERIFICATION_KEFF suite of criticality problems [1,2] was originally a set of 75 criticality problems found in the literature for which exact analytical solutions are available. Even though the spatial and energy detail is necessarily limited in analytical benchmarks, typically to a few regions or energy groups, the exact solutions obtained can be used to verify that the basic algorithms, mathematics, and methods used in complex production codes perform correctly. The present work has focused on revisiting this benchmark suite. A thorough review of the problems resulted in discarding some of them as not suitable for MCNP benchmarking. For the remaining problems, many of them were reformulated to permit execution in either multigroup mode or in the normal continuous-energy mode for MCNP. Execution of the benchmarks in continuous-energy mode provides a significant advance to MCNP verification methods.« less

A density-adaptive SPH method with kernel gradient correction for modeling explosive welding

NASA Astrophysics Data System (ADS)

Liu, M. B.; Zhang, Z. L.; Feng, D. L.

2017-09-01

Explosive welding involves processes like the detonation of explosive, impact of metal structures and strong fluid-structure interaction, while the whole process of explosive welding has not been well modeled before. In this paper, a novel smoothed particle hydrodynamics (SPH) model is developed to simulate explosive welding. In the SPH model, a kernel gradient correction algorithm is used to achieve better computational accuracy. A density adapting technique which can effectively treat large density ratio is also proposed. The developed SPH model is firstly validated by simulating a benchmark problem of one-dimensional TNT detonation and an impact welding problem. The SPH model is then successfully applied to simulate the whole process of explosive welding. It is demonstrated that the presented SPH method can capture typical physics in explosive welding including explosion wave, welding surface morphology, jet flow and acceleration of the flyer plate. The welding angle obtained from the SPH simulation agrees well with that from a kinematic analysis.

Characterizing Vegetation Model Skill and Uncertainty in Simulated Ecosystem Response to Climate Change in the United States

NASA Astrophysics Data System (ADS)

Drapek, R. J.; Kim, J. B.

2013-12-01

We simulated ecosystem response to climate change in the USA and Canada at a 5 arc-minute grid resolution using the MC1 dynamic global vegetation model and nine CMIP3 future climate projections as input. The climate projections were produced by 3 GCMs simulating 3 SRES emissions scenarios. We examined MC1 outputs for the conterminous USA by summarizing them by EPA level II and III ecoregions to characterize model skill and evaluate the magnitude and uncertainties of simulated ecosystem response to climate change. First, we evaluated model skill by comparing outputs from the recent historical period with benchmark datasets. Distribution of potential natural vegetation simulated by MC1 was compared with Kuchler's map. Above ground live carbon simulated by MC1 was compared with the National Biomass and Carbon Dataset. Fire return intervals calculated by MC1 were compared with maximum and minimum values compiled for the United States. Each EPA Level III Ecoregion was scored for average agreement with corresponding benchmark data and an average score was calculated for all three types of output. Greatest agreement with benchmark data happened in the Western Cordillera, the Ozark / Ouachita-Appalachian Forests, and the Southeastern USA Plains (EPA Level II Ecoregions). The lowest agreement happened in the Everglades and the Tamaulipas-Texas Semiarid Plain. For simulated ecosystem response to future climate projections we examined MC1 output for shifts in vegetation type, vegetation carbon, runoff, and biomass consumed by fire. Each ecoregion was scored for the amount of change from historical conditions for each variable and an average score was calculated. Smallest changes were forecast for Western Cordillera and Marine West Coast Forest ecosystems. Largest changes were forecast for the Cold Deserts, the Mixed Wood Plains, and the Central USA Plains. By combining scores of model skill for the historical period for each EPA Level 3 Ecoregion with scores representing the magnitude of ecosystem changes in the future, we identified high and low uncertainty ecoregions. The largest anticipated changes and the lowest measures of model skill coincide in the Central USA Plains and the Mixed Wood Plains. The combination of low model skill and high degree of ecosystem change elevate the importance of our uncertainty in this ecoregion. The highest projected changes coincide with relatively high model skill in the Cold Deserts. Climate adaptation efforts are the most likely to pay off in these regions. Finally, highest model skill and lowest anticipated changes coincide in the Western Cordillera and the Marine West Coast Forests. These regions may be relatively low-risk for climate change impacts when compared to the other ecoregions. These results represent only the first step in this type of analysis; there exist many ways to strengthen it. One, MC1 calibrations can be optimized using a structured optimization technique. Two, a larger set of climate projections can be used to capture a fuller range of GCMs and emissions scenarios. And three, employing an ensemble of vegetation models would make the analysis more robust.

Analogue experiments as benchmarks for models of lava flow emplacement

NASA Astrophysics Data System (ADS)

Garel, F.; Kaminski, E. C.; Tait, S.; Limare, A.

2013-12-01

During an effusive volcanic eruption, the crisis management is mainly based on the prediction of lava flow advance and its velocity. The spreading of a lava flow, seen as a gravity current, depends on its "effective rheology" and on the effusion rate. Fast-computing models have arisen in the past decade in order to predict in near real time lava flow path and rate of advance. This type of model, crucial to mitigate volcanic hazards and organize potential evacuation, has been mainly compared a posteriori to real cases of emplaced lava flows. The input parameters of such simulations applied to natural eruptions, especially effusion rate and topography, are often not known precisely, and are difficult to evaluate after the eruption. It is therefore not straightforward to identify the causes of discrepancies between model outputs and observed lava emplacement, whereas the comparison of models with controlled laboratory experiments appears easier. The challenge for numerical simulations of lava flow emplacement is to model the simultaneous advance and thermal structure of viscous lava flows. To provide original constraints later to be used in benchmark numerical simulations, we have performed lab-scale experiments investigating the cooling of isoviscous gravity currents. The simplest experimental set-up is as follows: silicone oil, whose viscosity, around 5 Pa.s, varies less than a factor of 2 in the temperature range studied, is injected from a point source onto a horizontal plate and spreads axisymmetrically. The oil is injected hot, and progressively cools down to ambient temperature away from the source. Once the flow is developed, it presents a stationary radial thermal structure whose characteristics depend on the input flow rate. In addition to the experimental observations, we have developed in Garel et al., JGR, 2012 a theoretical model confirming the relationship between supply rate, flow advance and stationary surface thermal structure. We also provide experimental observations of the effect of wind the surface thermal structure of a viscous flow, that could be used to benchmark a thermal heat loss model. We will also briefly present more complex analogue experiments using wax material. These experiments present discontinuous advance behavior, and a dual surface thermal structure with low (solidified) vs. high (hot liquid exposed at the surface) surface temperatures regions. Emplacement models should tend to reproduce these two features, also observed on lava flows, to better predict the hazard of lava inundation.

A Fast Visible-Infrared Imaging Radiometer Suite Simulator for Cloudy Atmopheres

NASA Technical Reports Server (NTRS)

Liu, Chao; Yang, Ping; Nasiri, Shaima L.; Platnick, Steven; Meyer, Kerry G.; Wang, Chen Xi; Ding, Shouguo

2015-01-01

A fast instrument simulator is developed to simulate the observations made in cloudy atmospheres by the Visible Infrared Imaging Radiometer Suite (VIIRS). The correlated k-distribution (CKD) technique is used to compute the transmissivity of absorbing atmospheric gases. The bulk scattering properties of ice clouds used in this study are based on the ice model used for the MODIS Collection 6 ice cloud products. Two fast radiative transfer models based on pre-computed ice cloud look-up-tables are used for the VIIRS solar and infrared channels. The accuracy and efficiency of the fast simulator are quantify in comparison with a combination of the rigorous line-by-line (LBLRTM) and discrete ordinate radiative transfer (DISORT) models. Relative errors are less than 2 for simulated TOA reflectances for the solar channels and the brightness temperature differences for the infrared channels are less than 0.2 K. The simulator is over three orders of magnitude faster than the benchmark LBLRTM+DISORT model. Furthermore, the cloudy atmosphere reflectances and brightness temperatures from the fast VIIRS simulator compare favorably with those from VIIRS observations.

Shallow water models as tool for tsunami current predictions in ports and harbors. Validation with Tohoku 2011 field data

NASA Astrophysics Data System (ADS)

Gonzalez Vida, J. M., Sr.; Macias Sanchez, J.; Castro, M. J.; Ortega, S.

2015-12-01

Model ability to compute and predict tsunami flow velocities is of importance in risk assessment and hazard mitigation. Substantial damage can be produced by high velocity flows, particularly in harbors and bays, even when the wave height is small. Besides, an accurate simulation of tsunami flow velocities and accelerations is fundamental for advancing in the study of tsunami sediment transport. These considerations made the National Tsunami Hazard Mitigation Program (NTHMP) proposing a benchmark exercise focused on modeling and simulating tsunami currents. Until recently, few direct measurements of tsunami velocities were available to compare and to validate model results. After Tohoku 2011 many current meters measurement were made, mainly in harbors and channels. In this work we present a part of the contribution made by the EDANYA group from the University of Malaga to the NTHMP workshop organized at Portland (USA), 9-10 of February 2015. We have selected three out of the five proposed benchmark problems. Two of them consist in real observed data from the Tohoku 2011 event, one at Hilo Habour (Hawaii) and the other at Tauranga Bay (New Zealand). The third one consists in laboratory experimental data for the inundation of Seaside City in Oregon. For this model validation the Tsunami-HySEA model, developed by EDANYA group, was used. The overall conclusion that we could extract from this validation exercise was that the Tsunami-HySEA model performed well in all benchmark problems proposed. The greater spatial variability in tsunami velocity than wave height makes it more difficult its precise numerical representation. The larger variability in velocities is likely a result of the behaviour of the flow as it is channelized and as it flows around bathymetric highs and structures. In the other hand wave height do not respond as strongly to chanelized flow as current velocity.

Benchmark of multi-phase method for the computation of fast ion distributions in a tokamak plasma in the presence of low-amplitude resonant MHD activity

NASA Astrophysics Data System (ADS)

Bierwage, A.; Todo, Y.

2017-11-01

The transport of fast ions in a beam-driven JT-60U tokamak plasma subject to resonant magnetohydrodynamic (MHD) mode activity is simulated using the so-called multi-phase method, where 4 ms intervals of classical Monte-Carlo simulations (without MHD) are interlaced with 1 ms intervals of hybrid simulations (with MHD). The multi-phase simulation results are compared to results obtained with continuous hybrid simulations, which were recently validated against experimental data (Bierwage et al., 2017). It is shown that the multi-phase method, in spite of causing significant overshoots in the MHD fluctuation amplitudes, accurately reproduces the frequencies and positions of the dominant resonant modes, as well as the spatial profile and velocity distribution of the fast ions, while consuming only a fraction of the computation time required by the continuous hybrid simulation. The present paper is limited to low-amplitude fluctuations consisting of a few long-wavelength modes that interact only weakly with each other. The success of this benchmark study paves the way for applying the multi-phase method to the simulation of Abrupt Large-amplitude Events (ALE), which were seen in the same JT-60U experiments but at larger time intervals. Possible implications for the construction of reduced models for fast ion transport are discussed.

Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment.

PubMed

Sim, Adelene Y L

2016-06-01

Nucleic acids are biopolymers that carry genetic information and are also involved in various gene regulation functions such as gene silencing and protein translation. Because of their negatively charged backbones, nucleic acids are polyelectrolytes. To adequately understand nucleic acid folding and function, we need to properly describe its i) polymer/polyelectrolyte properties and ii) associating ion atmosphere. While various theories and simulation models have been developed to describe nucleic acids and the ions around them, many of these theories/simulations have not been well evaluated due to complexities in comparison with experiment. In this review, I discuss some recent experiments that have been strategically designed for straightforward comparison with theories and simulation models. Such data serve as excellent benchmarks to identify limitations in prevailing theories and simulation parameters. Copyright © 2015 Elsevier B.V. All rights reserved.

The Model Averaging for Dichotomous Response Benchmark Dose (MADr-BMD) Tool

EPA Pesticide Factsheets

Providing quantal response models, which are also used in the U.S. EPA benchmark dose software suite, and generates a model-averaged dose response model to generate benchmark dose and benchmark dose lower bound estimates.

Finite difference time domain (FDTD) modeling of implanted deep brain stimulation electrodes and brain tissue.

PubMed

Gabran, S R I; Saad, J H; Salama, M M A; Mansour, R R

2009-01-01

This paper demonstrates the electromagnetic modeling and simulation of an implanted Medtronic deep brain stimulation (DBS) electrode using finite difference time domain (FDTD). The model is developed using Empire XCcel and represents the electrode surrounded with brain tissue assuming homogenous and isotropic medium. The model is created to study the parameters influencing the electric field distribution within the tissue in order to provide reference and benchmarking data for DBS and intra-cortical electrode development.

Biased ART: a neural architecture that shifts attention toward previously disregarded features following an incorrect prediction.

PubMed

Carpenter, Gail A; Gaddam, Sai Chaitanya

2010-04-01

Memories in Adaptive Resonance Theory (ART) networks are based on matched patterns that focus attention on those portions of bottom-up inputs that match active top-down expectations. While this learning strategy has proved successful for both brain models and applications, computational examples show that attention to early critical features may later distort memory representations during online fast learning. For supervised learning, biased ARTMAP (bARTMAP) solves the problem of over-emphasis on early critical features by directing attention away from previously attended features after the system makes a predictive error. Small-scale, hand-computed analog and binary examples illustrate key model dynamics. Two-dimensional simulation examples demonstrate the evolution of bARTMAP memories as they are learned online. Benchmark simulations show that featural biasing also improves performance on large-scale examples. One example, which predicts movie genres and is based, in part, on the Netflix Prize database, was developed for this project. Both first principles and consistent performance improvements on all simulation studies suggest that featural biasing should be incorporated by default in all ARTMAP systems. Benchmark datasets and bARTMAP code are available from the CNS Technology Lab Website: http://techlab.bu.edu/bART/. Copyright 2009 Elsevier Ltd. All rights reserved.

LAMMPS Project Report for the Trinity KNL Open Science Period.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moore, Stan Gerald; Thompson, Aidan P.; Wood, Mitchell

LAMMPS is a classical molecular dynamics code (lammps.sandia.gov) used to model materials science problems at Sandia National Laboratories and around the world. LAMMPS was one of three Sandia codes selected to participate in the Trinity KNL (TR2) Open Science period. During this period, three different problems of interest were investigated using LAMMPS. The first was benchmarking KNL performance using different force field models. The second was simulating void collapse in shocked HNS energetic material using an all-atom model. The third was simulating shock propagation through poly-crystalline RDX energetic material using a coarse-grain model, the results of which were used inmore » an ACM Gordon Bell Prize submission. This report describes the results of these simulations, lessons learned, and some hardware issues found on Trinity KNL as part of this work.« less

New Multi-group Transport Neutronics (PHISICS) Capabilities for RELAP5-3D and its Application to Phase I of the OECD/NEA MHTGR-350 MW Benchmark

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerhard Strydom; Cristian Rabiti; Andrea Alfonsi

2012-10-01

PHISICS is a neutronics code system currently under development at the Idaho National Laboratory (INL). Its goal is to provide state of the art simulation capability to reactor designers. The different modules for PHISICS currently under development are a nodal and semi-structured transport core solver (INSTANT), a depletion module (MRTAU) and a cross section interpolation (MIXER) module. The INSTANT module is the most developed of the mentioned above. Basic functionalities are ready to use, but the code is still in continuous development to extend its capabilities. This paper reports on the effort of coupling the nodal kinetics code package PHISICSmore » (INSTANT/MRTAU/MIXER) to the thermal hydraulics system code RELAP5-3D, to enable full core and system modeling. This will enable the possibility to model coupled (thermal-hydraulics and neutronics) problems with more options for 3D neutron kinetics, compared to the existing diffusion theory neutron kinetics module in RELAP5-3D (NESTLE). In the second part of the paper, an overview of the OECD/NEA MHTGR-350 MW benchmark is given. This benchmark has been approved by the OECD, and is based on the General Atomics 350 MW Modular High Temperature Gas Reactor (MHTGR) design. The benchmark includes coupled neutronics thermal hydraulics exercises that require more capabilities than RELAP5-3D with NESTLE offers. Therefore, the MHTGR benchmark makes extensive use of the new PHISICS/RELAP5-3D coupling capabilities. The paper presents the preliminary results of the three steady state exercises specified in Phase I of the benchmark using PHISICS/RELAP5-3D.« less

BSM2 Plant-Wide Model construction and comparative analysis with other methodologies for integrated modelling.

PubMed

Grau, P; Vanrolleghem, P; Ayesa, E

2007-01-01

In this paper, a new methodology for integrated modelling of the WWTP has been used for the construction of the Benchmark Simulation Model N degrees 2 (BSM2). The transformations-approach proposed in this methodology does not require the development of specific transformers to interface unit process models and allows the construction of tailored models for a particular WWTP guaranteeing the mass and charge continuity for the whole model. The BSM2 PWM constructed as case study, is evaluated by means of simulations under different scenarios and its validity in reproducing water and sludge lines in WWTP is demonstrated. Furthermore the advantages that this methodology presents compared to other approaches for integrated modelling are verified in terms of flexibility and coherence.

Verification and benchmark testing of the NUFT computer code

NASA Astrophysics Data System (ADS)

Lee, K. H.; Nitao, J. J.; Kulshrestha, A.

1993-10-01

This interim report presents results of work completed in the ongoing verification and benchmark testing of the NUFT (Nonisothermal Unsaturated-saturated Flow and Transport) computer code. NUFT is a suite of multiphase, multicomponent models for numerical solution of thermal and isothermal flow and transport in porous media, with application to subsurface contaminant transport problems. The code simulates the coupled transport of heat, fluids, and chemical components, including volatile organic compounds. Grid systems may be cartesian or cylindrical, with one-, two-, or fully three-dimensional configurations possible. In this initial phase of testing, the NUFT code was used to solve seven one-dimensional unsaturated flow and heat transfer problems. Three verification and four benchmarking problems were solved. In the verification testing, excellent agreement was observed between NUFT results and the analytical or quasianalytical solutions. In the benchmark testing, results of code intercomparison were very satisfactory. From these testing results, it is concluded that the NUFT code is ready for application to field and laboratory problems similar to those addressed here. Multidimensional problems, including those dealing with chemical transport, will be addressed in a subsequent report.

Determining Wheel-Soil Interaction Loads Using a Meshfree Finite Element Approach Assisting Future Missions with Rover Wheel Design

NASA Technical Reports Server (NTRS)

Contreras, Michael T.; Peng, Chia-Yen; Wang, Dongdong; Chen, Jiun-Shyan

2012-01-01

A wheel experiencing sinkage and slippage events poses a high risk to rover missions as evidenced by recent mobility challenges on the Mars Exploration Rover (MER) project. Because several factors contribute to wheel sinkage and slippage conditions such as soil composition, large deformation soil behavior, wheel geometry, nonlinear contact forces, terrain irregularity, etc., there are significant benefits to modeling these events to a sufficient degree of complexity. For the purposes of modeling wheel sinkage and slippage at an engineering scale, meshfree finite element approaches enable simulations that capture sufficient detail of wheel-soil interaction while remaining computationally feasible. This study demonstrates some of the large deformation modeling capability of meshfree methods and the realistic solutions obtained by accounting for the soil material properties. A benchmark wheel-soil interaction problem is developed and analyzed using a specific class of meshfree methods called Reproducing Kernel Particle Method (RKPM). The benchmark problem is also analyzed using a commercially available finite element approach with Lagrangian meshing for comparison. RKPM results are comparable to classical pressure-sinkage terramechanics relationships proposed by Bekker-Wong. Pending experimental calibration by future work, the meshfree modeling technique will be a viable simulation tool for trade studies assisting rover wheel design.

THE EFFECT OF BACKGROUND SIGNAL AND ITS REPRESENTATION IN DECONVOLUTION OF EPR SPECTRA ON ACCURACY OF EPR DOSIMETRY IN BONE.

PubMed

Ciesielski, Bartlomiej; Marciniak, Agnieszka; Zientek, Agnieszka; Krefft, Karolina; Cieszyński, Mateusz; Boguś, Piotr; Prawdzik-Dampc, Anita

2016-12-01

This study is about the accuracy of EPR dosimetry in bones based on deconvolution of the experimental spectra into the background (BG) and the radiation-induced signal (RIS) components. The model RIS's were represented by EPR spectra from irradiated enamel or bone powder; the model BG signals by EPR spectra of unirradiated bone samples or by simulated spectra. Samples of compact and trabecular bones were irradiated in the 30-270 Gy range and the intensities of their RIS's were calculated using various combinations of those benchmark spectra. The relationships between the dose and the RIS were linear (R 2  > 0.995), with practically no difference between results obtained when using signals from irradiated enamel or bone as the model RIS. Use of different experimental spectra for the model BG resulted in variations in intercepts of the dose-RIS calibration lines, leading to systematic errors in reconstructed doses, in particular for high- BG samples of trabecular bone. These errors were reduced when simulated spectra instead of the experimental ones were used as the benchmark BG signal in the applied deconvolution procedures. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

An Enriched Shell Finite Element for Progressive Damage Simulation in Composite Laminates

NASA Technical Reports Server (NTRS)

McElroy, Mark W.

2016-01-01

A formulation is presented for an enriched shell nite element capable of progressive damage simulation in composite laminates. The element uses a discrete adaptive splitting approach for damage representation that allows for a straightforward model creation procedure based on an initially low delity mesh. The enriched element is veri ed for Mode I, Mode II, and mixed Mode I/II delamination simulation using numerical benchmark data. Experimental validation is performed using test data from a delamination-migration experiment. Good correlation was found between the enriched shell element model results and the numerical and experimental data sets. The work presented in this paper is meant to serve as a rst milestone in the enriched element's development with an ultimate goal of simulating three-dimensional progressive damage processes in multidirectional laminates.

Benchmarking the MCNP code for Monte Carlo modelling of an in vivo neutron activation analysis system.

PubMed

Natto, S A; Lewis, D G; Ryde, S J

1998-01-01

The Monte Carlo computer code MCNP (version 4A) has been used to develop a personal computer-based model of the Swansea in vivo neutron activation analysis (IVNAA) system. The model included specification of the neutron source (252Cf), collimators, reflectors and shielding. The MCNP model was 'benchmarked' against fast neutron and thermal neutron fluence data obtained experimentally from the IVNAA system. The Swansea system allows two irradiation geometries using 'short' and 'long' collimators, which provide alternative dose rates for IVNAA. The data presented here relate to the short collimator, although results of similar accuracy were obtained using the long collimator. The fast neutron fluence was measured in air at a series of depths inside the collimator. The measurements agreed with the MCNP simulation within the statistical uncertainty (5-10%) of the calculations. The thermal neutron fluence was measured and calculated inside the cuboidal water phantom. The depth of maximum thermal fluence was 3.2 cm (measured) and 3.0 cm (calculated). The width of the 50% thermal fluence level across the phantom at its mid-depth was found to be the same by both MCNP and experiment. This benchmarking exercise has given us a high degree of confidence in MCNP as a tool for the design of IVNAA systems.

Parameter Estimation of Actuators for Benchmark Active Control Technology (BACT) Wind Tunnel Model with Analysis of Wear and Aerodynamic Loading Effects

NASA Technical Reports Server (NTRS)

Waszak, Martin R.; Fung, Jimmy

1998-01-01

This report describes the development of transfer function models for the trailing-edge and upper and lower spoiler actuators of the Benchmark Active Control Technology (BACT) wind tunnel model for application to control system analysis and design. A simple nonlinear least-squares parameter estimation approach is applied to determine transfer function parameters from frequency response data. Unconstrained quasi-Newton minimization of weighted frequency response error was employed to estimate the transfer function parameters. An analysis of the behavior of the actuators over time to assess the effects of wear and aerodynamic load by using the transfer function models is also presented. The frequency responses indicate consistent actuator behavior throughout the wind tunnel test and only slight degradation in effectiveness due to aerodynamic hinge loading. The resulting actuator models have been used in design, analysis, and simulation of controllers for the BACT to successfully suppress flutter over a wide range of conditions.

Computer simulation of multigrid body dynamics and control

NASA Technical Reports Server (NTRS)

Swaminadham, M.; Moon, Young I.; Venkayya, V. B.

1990-01-01

The objective is to set up and analyze benchmark problems on multibody dynamics and to verify the predictions of two multibody computer simulation codes. TREETOPS and DISCOS have been used to run three example problems - one degree-of-freedom spring mass dashpot system, an inverted pendulum system, and a triple pendulum. To study the dynamics and control interaction, an inverted planar pendulum with an external body force and a torsional control spring was modeled as a hinge connected two-rigid body system. TREETOPS and DISCOS affected the time history simulation of this problem. System state space variables and their time derivatives from two simulation codes were compared.

Characterizing Wheel-Soil Interaction Loads Using Meshfree Finite Element Methods: A Sensitivity Analysis for Design Trade Studies

NASA Technical Reports Server (NTRS)

Contreras, Michael T.; Trease, Brian P.; Bojanowski, Cezary; Kulakx, Ronald F.

2013-01-01

A wheel experiencing sinkage and slippage events poses a high risk to planetary rover missions as evidenced by the mobility challenges endured by the Mars Exploration Rover (MER) project. Current wheel design practice utilizes loads derived from a series of events in the life cycle of the rover which do not include (1) failure metrics related to wheel sinkage and slippage and (2) performance trade-offs based on grouser placement/orientation. Wheel designs are rigorously tested experimentally through a variety of drive scenarios and simulated soil environments; however, a robust simulation capability is still in development due to myriad of complex interaction phenomena that contribute to wheel sinkage and slippage conditions such as soil composition, large deformation soil behavior, wheel geometry, nonlinear contact forces, terrain irregularity, etc. For the purposes of modeling wheel sinkage and slippage at an engineering scale, meshfree nite element approaches enable simulations that capture su cient detail of wheel-soil interaction while remaining computationally feasible. This study implements the JPL wheel-soil benchmark problem in the commercial code environment utilizing the large deformation modeling capability of Smooth Particle Hydrodynamics (SPH) meshfree methods. The nominal, benchmark wheel-soil interaction model that produces numerically stable and physically realistic results is presented and simulations are shown for both wheel traverse and wheel sinkage cases. A sensitivity analysis developing the capability and framework for future ight applications is conducted to illustrate the importance of perturbations to critical material properties and parameters. Implementation of the proposed soil-wheel interaction simulation capability and associated sensitivity framework has the potential to reduce experimentation cost and improve the early stage wheel design proce

Establishing objective benchmarks in robotic virtual reality simulation at the level of a competent surgeon using the RobotiX Mentor simulator.

PubMed

Watkinson, William; Raison, Nicholas; Abe, Takashige; Harrison, Patrick; Khan, Shamim; Van der Poel, Henk; Dasgupta, Prokar; Ahmed, Kamran

2018-05-01

To establish objective benchmarks at the level of a competent robotic surgeon across different exercises and metrics for the RobotiX Mentor virtual reality (VR) simulator suitable for use within a robotic surgical training curriculum. This retrospective observational study analysed results from multiple data sources, all of which used the RobotiX Mentor VR simulator. 123 participants with varying experience from novice to expert completed the exercises. Competency was established as the 25th centile of the mean advanced intermediate score. Three basic skill exercises and two advanced skill exercises were used. King's College London. 84 Novice, 26 beginner intermediates, 9 advanced intermediates and 4 experts were used in this retrospective observational study. Objective benchmarks derived from the 25th centile of the mean scores of the advanced intermediates provided suitably challenging yet also achievable targets for training surgeons. The disparity in scores was greatest for the advanced exercises. Novice surgeons are able to achieve the benchmarks across all exercises in the majority of metrics. We have successfully created this proof-of-concept study, which requires validation in a larger cohort. Objective benchmarks obtained from the 25th centile of the mean scores of advanced intermediates provide clinically relevant benchmarks at the standard of a competent robotic surgeon that are challenging yet also attainable. That can be used within a VR training curriculum allowing participants to track and monitor their progress in a structured and progressional manner through five exercises. Providing clearly defined targets, ensuring that a universal training standard has been achieved across training surgeons. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Access to a simulator is not enough: the benefits of virtual reality training based on peer-group-derived benchmarks--a randomized controlled trial.

PubMed

von Websky, Martin W; Raptis, Dimitri A; Vitz, Martina; Rosenthal, Rachel; Clavien, P A; Hahnloser, Dieter

2013-11-01

Virtual reality (VR) simulators are widely used to familiarize surgical novices with laparoscopy, but VR training methods differ in efficacy. In the present trial, self-controlled basic VR training (SC-training) was tested against training based on peer-group-derived benchmarks (PGD-training). First, novice laparoscopic residents were randomized into a SC group (n = 34), and a group using PGD-benchmarks (n = 34) for basic laparoscopic training. After completing basic training, both groups performed 60 VR laparoscopic cholecystectomies for performance analysis. Primary endpoints were simulator metrics; secondary endpoints were program adherence, trainee motivation, and training efficacy. Altogether, 66 residents completed basic training, and 3,837 of 3,960 (96.8 %) cholecystectomies were available for analysis. Course adherence was good, with only two dropouts, both in the SC-group. The PGD-group spent more time and repetitions in basic training until the benchmarks were reached and subsequently showed better performance in the readout cholecystectomies: Median time (gallbladder extraction) showed significant differences of 520 s (IQR 354-738 s) in SC-training versus 390 s (IQR 278-536 s) in the PGD-group (p < 0.001) and 215 s (IQR 175-276 s) in experts, respectively. Path length of the right instrument also showed significant differences, again with the PGD-training group being more efficient. Basic VR laparoscopic training based on PGD benchmarks with external assessment is superior to SC training, resulting in higher trainee motivation and better performance in simulated laparoscopic cholecystectomies. We recommend such a basic course based on PGD benchmarks before advancing to more elaborate VR training.

A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator

DOE PAGES

Engelmann, Christian; Naughton, III, Thomas J.

2016-03-22

Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different HPC architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1)~a new deadlock resolution protocol to reduce the parallel discrete event simulation overhead and (2)~a new simulated MPI message matchingmore » algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement. The simulation overhead for running the NAS Parallel Benchmark suite was reduced from 102% to 0% for the embarrassingly parallel (EP) benchmark and from 1,020% to 238% for the conjugate gradient (CG) benchmark. xSim offers a highly accurate simulation mode for better tracking of injected MPI process failures. Furthermore, with highly accurate simulation, the overhead was reduced from 3,332% to 204% for EP and from 37,511% to 13,808% for CG.« less

Shadow: Running Tor in a Box for Accurate and Efficient Experimentation

DTIC Science & Technology

2011-09-23

Modeling the speed of a target CPU is done by running an OpenSSL [31] speed test on a real CPU of that type. This provides us with the raw CPU processing...rate, but we are also interested in the processing speed of an application. By running application 5 benchmarks on the same CPU as the OpenSSL speed test...simulation, saving CPU cy- cles on our simulation host machine. Shadow removes cryptographic processing by preloading the main OpenSSL [31] functions used

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics.

PubMed

Strehl, Robert; Ilie, Silvana

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

New methods to benchmark simulations of accreting black holes systems against observations

NASA Astrophysics Data System (ADS)

Markoff, Sera; Chatterjee, Koushik; Liska, Matthew; Tchekhovskoy, Alexander; Hesp, Casper; Ceccobello, Chiara; Russell, Thomas

2017-08-01

The field of black hole accretion has been significantly advanced by the use of complex ideal general relativistic magnetohydrodynamics (GRMHD) codes, now capable of simulating scales from the event horizon out to ~10^5 gravitational radii at high resolution. The challenge remains how to test these simulations against data, because the self-consistent treatment of radiation is still in its early days, and is complicated by dependence on non-ideal/microphysical processes not yet included in the codes. On the other extreme, a variety of phenomenological models (disk, corona, jet, wind) can well-describe spectra or variability signatures in a particular waveband, although often not both. To bring these two methodologies together, we need robust observational “benchmarks” that can be identified and studied in simulations. I will focus on one example of such a benchmark, from recent observational campaigns on black holes across the mass scale: the jet break. I will describe new work attempting to understand what drives this feature by searching for regions that share similar trends in terms of dependence on accretion power or magnetisation. Such methods can allow early tests of simulation assumptions and help pinpoint which regions will dominate the light production, well before full radiative processes are incorporated, and will help guide the interpretation of, e.g. Event Horizon Telescope data.

Efficient Modeling of Laser-Plasma Accelerators with INF and RNO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benedetti, C.; Schroeder, C. B.; Esarey, E.

2010-11-04

The numerical modeling code INF and RNO (INtegrated Fluid and paRticle simulatioN cOde, pronounced 'inferno') is presented. INF and RNO is an efficient 2D cylindrical code to model the interaction of a short laser pulse with an underdense plasma. The code is based on an envelope model for the laser while either a PIC or a fluid description can be used for the plasma. The effect of the laser pulse on the plasma is modeled with the time-averaged poderomotive force. These and other features allow for a speedup of 2-4 orders of magnitude compared to standard full PIC simulations whilemore » still retaining physical fidelity. The code has been benchmarked against analytical solutions and 3D PIC simulations and here a set of validation tests together with a discussion of the performances are presented.« less

Discrete ellipsoidal statistical BGK model and Burnett equations

NASA Astrophysics Data System (ADS)

Zhang, Yu-Dong; Xu, Ai-Guo; Zhang, Guang-Cai; Chen, Zhi-Hua; Wang, Pei

2018-06-01

A new discrete Boltzmann model, the discrete ellipsoidal statistical Bhatnagar-Gross-Krook (ESBGK) model, is proposed to simulate nonequilibrium compressible flows. Compared with the original discrete BGK model, the discrete ES-BGK has a flexible Prandtl number. For the discrete ES-BGK model in the Burnett level, two kinds of discrete velocity model are introduced and the relations between nonequilibrium quantities and the viscous stress and heat flux in the Burnett level are established. The model is verified via four benchmark tests. In addition, a new idea is introduced to recover the actual distribution function through the macroscopic quantities and their space derivatives. The recovery scheme works not only for discrete Boltzmann simulation but also for hydrodynamic ones, for example, those based on the Navier-Stokes or the Burnett equations.

GLOFRIM - A globally applicable framework for integrated hydrologic-hydrodynamic inundation modelling

NASA Astrophysics Data System (ADS)

Hoch, J. M.; Neal, J. C.; Baart, F.; Van Beek, L. P.; Winsemius, H.; Bates, P. D.; Bierkens, M. F.

2017-12-01

Currently, many approaches to provide detailed flood hazard and risk estimates are built upon specific hydrologic or hydrodynamic model routines. By applying these routines in stand-alone mode important processes can however not accurately be described. For instance, global hydrologic models run at coarse spatial resolution, not supporting the detailed simulation of flood hazard. Hydrodynamic models excel in the computations of open water flow dynamics, but dependent on specific runoff or observed discharge as input. In most cases hydrodynamic models are forced at the boundaries and thus cannot account for water sources within the model domain, limiting the simulation of inundation dynamics to reaches fed by upstream boundaries. Recently, Hoch et al. (HESS, 2017) coupled PCR-GLOBWB (PCR) with the hydrodynamic model Delft3D Flexible Mesh (DFM). By means of the Basic Model Interface both models were connected on a cell-by-cell basis, allowing for spatially explicit coupling. Model results showed that discharge simulations can profit from model coupling compared to stand-alone runs. As model results of a coupled simulation depend on the quality of the models, it would be worthwhile to allow a suite of models to be coupled. To facilitate this, we present GLOFRIM, a globally applicable framework for integrated hydrologic-hydrodynamic inundation modelling. In the current version coupling between PCR and both DFM and LISFLOOD-FP (LFP) can be established (Hoch et al., GMDD, 2017). First results show that differences between both hydrodynamic models are present in the timing of peak discharge which is most likely due to differences in channel-floodplain interactions and bathymetry processing. Having benchmarked inundation extent, LFP and DFM agree for around half of the inundated area which is attributable to variations in grid size. Results also indicate that, despite using identical boundary conditions and forcing, the schematization itself as well as internal processes can still greatly influence results. In general, the application of GLOFRIM brings several advantages. For example, with PCR being a global model, it is possible to reduce the dependency of observation data for discharge boundaries, and benchmarking of hydrodynamic models is greatly facilitated by employing identical hydrologic forcing.

multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions.

PubMed

Kang, Guangliang; Du, Li; Zhang, Hong

2016-06-22

The growing complexity of biological experiment design based on high-throughput RNA sequencing (RNA-seq) is calling for more accommodative statistical tools. We focus on differential expression (DE) analysis using RNA-seq data in the presence of multiple treatment conditions. We propose a novel method, multiDE, for facilitating DE analysis using RNA-seq read count data with multiple treatment conditions. The read count is assumed to follow a log-linear model incorporating two factors (i.e., condition and gene), where an interaction term is used to quantify the association between gene and condition. The number of the degrees of freedom is reduced to one through the first order decomposition of the interaction, leading to a dramatically power improvement in testing DE genes when the number of conditions is greater than two. In our simulation situations, multiDE outperformed the benchmark methods (i.e. edgeR and DESeq2) even if the underlying model was severely misspecified, and the power gain was increasing in the number of conditions. In the application to two real datasets, multiDE identified more biologically meaningful DE genes than the benchmark methods. An R package implementing multiDE is available publicly at http://homepage.fudan.edu.cn/zhangh/softwares/multiDE . When the number of conditions is two, multiDE performs comparably with the benchmark methods. When the number of conditions is greater than two, multiDE outperforms the benchmark methods.

U.S. IOOS coastal and ocean modeling testbed: Inter-model evaluation of tides, waves, and hurricane surge in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Kerr, P. C.; Donahue, A. S.; Westerink, J. J.; Luettich, R. A.; Zheng, L. Y.; Weisberg, R. H.; Huang, Y.; Wang, H. V.; Teng, Y.; Forrest, D. R.; Roland, A.; Haase, A. T.; Kramer, A. W.; Taylor, A. A.; Rhome, J. R.; Feyen, J. C.; Signell, R. P.; Hanson, J. L.; Hope, M. E.; Estes, R. M.; Dominguez, R. A.; Dunbar, R. P.; Semeraro, L. N.; Westerink, H. J.; Kennedy, A. B.; Smith, J. M.; Powell, M. D.; Cardone, V. J.; Cox, A. T.

2013-10-01

A Gulf of Mexico performance evaluation and comparison of coastal circulation and wave models was executed through harmonic analyses of tidal simulations, hindcasts of Hurricane Ike (2008) and Rita (2005), and a benchmarking study. Three unstructured coastal circulation models (ADCIRC, FVCOM, and SELFE) validated with similar skill on a new common Gulf scale mesh (ULLR) with identical frictional parameterization and forcing for the tidal validation and hurricane hindcasts. Coupled circulation and wave models, SWAN+ADCIRC and WWMII+SELFE, along with FVCOM loosely coupled with SWAN, also validated with similar skill. NOAA's official operational forecast storm surge model (SLOSH) was implemented on local and Gulf scale meshes with the same wind stress and pressure forcing used by the unstructured models for hindcasts of Ike and Rita. SLOSH's local meshes failed to capture regional processes such as Ike's forerunner and the results from the Gulf scale mesh further suggest shortcomings may be due to a combination of poor mesh resolution, missing internal physics such as tides and nonlinear advection, and SLOSH's internal frictional parameterization. In addition, these models were benchmarked to assess and compare execution speed and scalability for a prototypical operational simulation. It was apparent that a higher number of computational cores are needed for the unstructured models to meet similar operational implementation requirements to SLOSH, and that some of them could benefit from improved parallelization and faster execution speed.

CAFE simulation of columnar-to-equiaxed transition in Al-7wt%Si alloys directionally solidified under microgravity

NASA Astrophysics Data System (ADS)

Liu, D. R.; Mangelinck-Noël, N.; Gandin, Ch-A.; Zimmermann, G.; Sturz, L.; Nguyen Thi, H.; Billia, B.

2016-03-01

A two-dimensional multi-scale cellular automaton - finite element (CAFE) model is used to simulate grain structure evolution and microsegregation formation during solidification of refined Al-7wt%Si alloys under microgravity. The CAFE simulations are first qualitatively compared with the benchmark experimental data under microgravity. Qualitative agreement is obtained for the position of columnar to equiaxed transition (CET) and the CET transition mode (sharp or progressive). Further comparisons of the distributions of grain elongation factor and equivalent diameter are conducted and reveal a fair quantitative agreement.

A conservative approach to parallelizing the Sharks World simulation

NASA Technical Reports Server (NTRS)

Nicol, David M.; Riffe, Scott E.

1990-01-01

Parallelizing a benchmark problem for parallel simulation, the Sharks World, is described. The described solution is conservative, in the sense that no state information is saved, and no 'rollbacks' occur. The used approach illustrates both the principal advantage and principal disadvantage of conservative parallel simulation. The advantage is that by exploiting lookahead an approach was found that dramatically improves the serial execution time, and also achieves excellent speedups. The disadvantage is that if the model rules are changed in such a way that the lookahead is destroyed, it is difficult to modify the solution to accommodate the changes.

Four-Nozzle Benchmark Wind Tunnel Model USA Code Solutions for Simulation of Multiple Rocket Base Flow Recirculation at 145,000 Feet Altitude

NASA Technical Reports Server (NTRS)

Dougherty, N. S.; Johnson, S. L.

1993-01-01

Multiple rocket exhaust plume interactions at high altitudes can produce base flow recirculation with attendant alteration of the base pressure coefficient and increased base heating. A search for a good wind tunnel benchmark problem to check grid clustering technique and turbulence modeling turned up the experiment done at AEDC in 1961 by Goethert and Matz on a 4.25-in. diameter domed missile base model with four rocket nozzles. This wind tunnel model with varied external bleed air flow for the base flow wake produced measured p/p(sub ref) at the center of the base as high as 3.3 due to plume flow recirculation back onto the base. At that time in 1961, relatively inexpensive experimentation with air at gamma = 1.4 and nozzle A(sub e)/A of 10.6 and theta(sub n) = 7.55 deg with P(sub c) = 155 psia simulated a LO2/LH2 rocket exhaust plume with gamma = 1.20, A(sub e)/A of 78 and P(sub c) about 1,000 psia. An array of base pressure taps on the aft dome gave a clear measurement of the plume recirculation effects at p(infinity) = 4.76 psfa corresponding to 145,000 ft altitude. Our CFD computations of the flow field with direct comparison of computed-versus-measured base pressure distribution (across the dome) provide detailed information on velocities and particle traces as well eddy viscosity in the base and nozzle region. The solution was obtained using a six-zone mesh with 284,000 grid points for one quadrant taking advantage of symmetry. Results are compared using a zero-equation algebraic and a one-equation pointwise R(sub t) turbulence model (work in progress). Good agreement with the experimental pressure data was obtained with both; and this benchmark showed the importance of: (1) proper grid clustering and (2) proper choice of turbulence modeling for rocket plume problems/recirculation at high altitude.

The Isprs Benchmark on Indoor Modelling

NASA Astrophysics Data System (ADS)

Khoshelham, K.; Díaz Vilariño, L.; Peter, M.; Kang, Z.; Acharya, D.

2017-09-01

Automated generation of 3D indoor models from point cloud data has been a topic of intensive research in recent years. While results on various datasets have been reported in literature, a comparison of the performance of different methods has not been possible due to the lack of benchmark datasets and a common evaluation framework. The ISPRS benchmark on indoor modelling aims to address this issue by providing a public benchmark dataset and an evaluation framework for performance comparison of indoor modelling methods. In this paper, we present the benchmark dataset comprising several point clouds of indoor environments captured by different sensors. We also discuss the evaluation and comparison of indoor modelling methods based on manually created reference models and appropriate quality evaluation criteria. The benchmark dataset is available for download at: http://www2.isprs.org/commissions/comm4/wg5/benchmark-on-indoor-modelling.html.

PrimeSupplier Cross-Program Impact Analysis and Supplier Stability Indicator Simulation Model

NASA Technical Reports Server (NTRS)

Calluzzi, Michael

2009-01-01

PrimeSupplier, a supplier cross-program and element-impact simulation model, with supplier solvency indicator (SSI), has been developed so that the shuttle program can see early indicators of supplier and product line stability, while identifying the various elements and/or programs that have a particular supplier or product designed into the system. The model calculates two categories of benchmarks to determine the SSI, with one category focusing on agency programmatic data and the other focusing on a supplier's financial liquidity. PrimeSupplier was developed to help NASA smoothly transition design, manufacturing, and repair operations from the Shuttle program to the Constellation program, without disruption in the industrial supply base.

Ice Accretion Modeling using an Eulerian Approach for Droplet Impingement

NASA Technical Reports Server (NTRS)

Kim, Joe Woong; Garza, Dennis P.; Sankar, Lakshmi N.; Kreeger, Richard E.

2012-01-01

A three-dimensional Eulerian analysis has been developed for modeling droplet impingement on lifting bodes. The Eulerian model solves the conservation equations of mass and momentum to obtain the droplet flow field properties on the same mesh used in CFD simulations. For complex configurations such as a full rotorcraft, the Eulerian approach is more efficient because the Lagrangian approach would require a significant amount of seeding for accurate estimates of collection efficiency. Simulations are done for various benchmark cases such as NACA0012 airfoil, MS317 airfoil and oscillating SC2110 airfoil to illustrate its use. The present results are compared with results from the Lagrangian approach used in an industry standard analysis called LEWICE.

Data-driven train set crash dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, Zhao; Zhu, Yunrui; Nie, Yinyu; Guo, Shihui; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2017-02-01

Traditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force-displacement curves and predicts a force-displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency.

Main steam line break accident simulation of APR1400 using the model of ATLAS facility

NASA Astrophysics Data System (ADS)

Ekariansyah, A. S.; Deswandri; Sunaryo, Geni R.

2018-02-01

A main steam line break simulation for APR1400 as an advanced design of PWR has been performed using the RELAP5 code. The simulation was conducted in a model of thermal-hydraulic test facility called as ATLAS, which represents a scaled down facility of the APR1400 design. The main steam line break event is described in a open-access safety report document, in which initial conditions and assumptionsfor the analysis were utilized in performing the simulation and analysis of the selected parameter. The objective of this work was to conduct a benchmark activities by comparing the simulation results of the CESEC-III code as a conservative approach code with the results of RELAP5 as a best-estimate code. Based on the simulation results, a general similarity in the behavior of selected parameters was observed between the two codes. However the degree of accuracy still needs further research an analysis by comparing with the other best-estimate code. Uncertainties arising from the ATLAS model should be minimized by taking into account much more specific data in developing the APR1400 model.

High performance cellular level agent-based simulation with FLAME for the GPU.

PubMed

Richmond, Paul; Walker, Dawn; Coakley, Simon; Romano, Daniela

2010-05-01

Driven by the availability of experimental data and ability to simulate a biological scale which is of immediate interest, the cellular scale is fast emerging as an ideal candidate for middle-out modelling. As with 'bottom-up' simulation approaches, cellular level simulations demand a high degree of computational power, which in large-scale simulations can only be achieved through parallel computing. The flexible large-scale agent modelling environment (FLAME) is a template driven framework for agent-based modelling (ABM) on parallel architectures ideally suited to the simulation of cellular systems. It is available for both high performance computing clusters (www.flame.ac.uk) and GPU hardware (www.flamegpu.com) and uses a formal specification technique that acts as a universal modelling format. This not only creates an abstraction from the underlying hardware architectures, but avoids the steep learning curve associated with programming them. In benchmarking tests and simulations of advanced cellular systems, FLAME GPU has reported massive improvement in performance over more traditional ABM frameworks. This allows the time spent in the development and testing stages of modelling to be drastically reduced and creates the possibility of real-time visualisation for simple visual face-validation.

Vehicle Component Benchmarking Using a Chassis Dynamometer: Using a 2013 Chevrolet Malibu and a 2013 Mercedes E350 (SAE Paper 2015-01-0589)

EPA Science Inventory

Light-duty vehicle greenhouse gas (GHG) and fuel economy (FE) standards for MYs 2012 -2025 are requiring vehicle powertrains to become much more efficient. The EPA is using a full vehicle simulation model, called the Advanced Light-duty Powertrain and Hybrid Analysis (ALPHA), to ...

An overview of the ENEA activities in the field of coupled codes NPP simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parisi, C.; Negrenti, E.; Sepielli, M.

2012-07-01

In the framework of the nuclear research activities in the fields of safety, training and education, ENEA (the Italian National Agency for New Technologies, Energy and the Sustainable Development) is in charge of defining and pursuing all the necessary steps for the development of a NPP engineering simulator at the 'Casaccia' Research Center near Rome. A summary of the activities in the field of the nuclear power plants simulation by coupled codes is here presented with the long term strategy for the engineering simulator development. Specifically, results from the participation in international benchmarking activities like the OECD/NEA 'Kalinin-3' benchmark andmore » the 'AER-DYN-002' benchmark, together with simulations of relevant events like the Fukushima accident, are here reported. The ultimate goal of such activities performed using state-of-the-art technology is the re-establishment of top level competencies in the NPP simulation field in order to facilitate the development of Enhanced Engineering Simulators and to upgrade competencies for supporting national energy strategy decisions, the nuclear national safety authority, and the R and D activities on NPP designs. (authors)« less

Development of a sensor coordinated kinematic model for neural network controller training

NASA Technical Reports Server (NTRS)

Jorgensen, Charles C.

1990-01-01

A robotic benchmark problem useful for evaluating alternative neural network controllers is presented. Specifically, it derives two camera models and the kinematic equations of a multiple degree of freedom manipulator whose end effector is under observation. The mapping developed include forward and inverse translations from binocular images to 3-D target position and the inverse kinematics of mapping point positions into manipulator commands in joint space. Implementation is detailed for a three degree of freedom manipulator with one revolute joint at the base and two prismatic joints on the arms. The example is restricted to operate within a unit cube with arm links of 0.6 and 0.4 units respectively. The development is presented in the context of more complex simulations and a logical path for extension of the benchmark to higher degree of freedom manipulators is presented.

Coherent dynamic structure factors of strongly coupled plasmas: A generalized hydrodynamic approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Di; Hu, GuangYue; Gong, Tao

2016-05-15

A generalized hydrodynamic fluctuation model is proposed to simplify the calculation of the dynamic structure factor S(ω, k) of non-ideal plasmas using the fluctuation-dissipation theorem. In this model, the kinetic and correlation effects are both included in hydrodynamic coefficients, which are considered as functions of the coupling strength (Γ) and collision parameter (kλ{sub ei}), where λ{sub ei} is the electron-ion mean free path. A particle-particle particle-mesh molecular dynamics simulation code is also developed to simulate the dynamic structure factors, which are used to benchmark the calculation of our model. A good agreement between the two different approaches confirms the reliabilitymore » of our model.« less

Atomization simulations using an Eulerian-VOF-Lagrangian method

NASA Technical Reports Server (NTRS)

Chen, Yen-Sen; Shang, Huan-Min; Liaw, Paul; Chen, C. P.

1994-01-01

This paper summarizes the technical development and validation of a multiphase computational fluid dynamics (CFD) numerical method using the volume-of-fluid (VOF) model and a Lagrangian tracking model which can be employed to analyze general multiphase flow problems with free surface mechanism. The gas-liquid interface mass, momentum and energy conservations are modeled by continuum surface mechanisms. A new solution method is developed such that the present VOF model can be applied for all-speed flow regimes. The objectives of the present study are to develop and verify the fractional volume-of-fluid cell partitioning approach into a predictor-corrector algorithm and to demonstrate the effectiveness of the present innovative approach by simulating benchmark problems including the coaxial jet atomization.

[Benchmark experiment to verify radiation transport calculations for dosimetry in radiation therapy].

PubMed

Renner, Franziska

2016-09-01

Monte Carlo simulations are regarded as the most accurate method of solving complex problems in the field of dosimetry and radiation transport. In (external) radiation therapy they are increasingly used for the calculation of dose distributions during treatment planning. In comparison to other algorithms for the calculation of dose distributions, Monte Carlo methods have the capability of improving the accuracy of dose calculations - especially under complex circumstances (e.g. consideration of inhomogeneities). However, there is a lack of knowledge of how accurate the results of Monte Carlo calculations are on an absolute basis. A practical verification of the calculations can be performed by direct comparison with the results of a benchmark experiment. This work presents such a benchmark experiment and compares its results (with detailed consideration of measurement uncertainty) with the results of Monte Carlo calculations using the well-established Monte Carlo code EGSnrc. The experiment was designed to have parallels to external beam radiation therapy with respect to the type and energy of the radiation, the materials used and the kind of dose measurement. Because the properties of the beam have to be well known in order to compare the results of the experiment and the simulation on an absolute basis, the benchmark experiment was performed using the research electron accelerator of the Physikalisch-Technische Bundesanstalt (PTB), whose beam was accurately characterized in advance. The benchmark experiment and the corresponding Monte Carlo simulations were carried out for two different types of ionization chambers and the results were compared. Considering the uncertainty, which is about 0.7 % for the experimental values and about 1.0 % for the Monte Carlo simulation, the results of the simulation and the experiment coincide. Copyright © 2015. Published by Elsevier GmbH.

Primesupplier Podcast

NASA Technical Reports Server (NTRS)

Galluzzi, Michael; Ferrari, Pasquale; Fair, Jennifer

2009-01-01

PrimeSupplier, s supplier cross program and element impact simulation model with supplier solvency indicator (SSI), has been developed so that the Shuttle Program can see an early indicator of supplier and product line stability while identifying the various elements and/or programs that have a particular supplier of product designed into the system. The model calculates two categories of benchmarks to determine the SSI with one category focusing on Agency programmatic and the other being a supplier financial liquidity.

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

DTIC Science & Technology

2017-01-10

benchmarks of conformational sampling methods and their all-atom force fields plus solvent descriptions to accurately model structural transitions on a...atom simulations of proteins is the replacement of explicit water interactions with a continuum description of treating implicitly the bulk physical... structure was reported by Amarasinghe and coworkers (Leung et al., 2015) of the Ebola nucleoprotein NP in complex with a 28-residue peptide extracted

Verification of ARES transport code system with TAKEDA benchmarks

NASA Astrophysics Data System (ADS)

Zhang, Liang; Zhang, Bin; Zhang, Penghe; Chen, Mengteng; Zhao, Jingchang; Zhang, Shun; Chen, Yixue

2015-10-01

Neutron transport modeling and simulation are central to many areas of nuclear technology, including reactor core analysis, radiation shielding and radiation detection. In this paper the series of TAKEDA benchmarks are modeled to verify the critical calculation capability of ARES, a discrete ordinates neutral particle transport code system. SALOME platform is coupled with ARES to provide geometry modeling and mesh generation function. The Koch-Baker-Alcouffe parallel sweep algorithm is applied to accelerate the traditional transport calculation process. The results show that the eigenvalues calculated by ARES are in excellent agreement with the reference values presented in NEACRP-L-330, with a difference less than 30 pcm except for the first case of model 3. Additionally, ARES provides accurate fluxes distribution compared to reference values, with a deviation less than 2% for region-averaged fluxes in all cases. All of these confirms the feasibility of ARES-SALOME coupling and demonstrate that ARES has a good performance in critical calculation.

A Fully Nonlinear, Dynamically Consistent Numerical Model for Solid-Body Ship Motion. I. Ship Motion with Fixed Heading

NASA Technical Reports Server (NTRS)

Lin, Ray-Quing; Kuang, Weijia

2011-01-01

In this paper, we describe the details of our numerical model for simulating ship solidbody motion in a given environment. In this model, the fully nonlinear dynamical equations governing the time-varying solid-body ship motion under the forces arising from ship wave interactions are solved with given initial conditions. The net force and moment (torque) on the ship body are directly calculated via integration of the hydrodynamic pressure over the wetted surface and the buoyancy effect from the underwater volume of the actual ship hull with a hybrid finite-difference/finite-element method. Neither empirical nor free parametrization is introduced in this model, i.e. no a priori experimental data are needed for modelling. This model is benchmarked with many experiments of various ship hulls for heave, roll and pitch motion. In addition to the benchmark cases, numerical experiments are also carried out for strongly nonlinear ship motion with a fixed heading. These new cases demonstrate clearly the importance of nonlinearities in ship motion modelling.

Revisiting Turbulence Model Validation for High-Mach Number Axisymmetric Compression Corner Flows

NASA Technical Reports Server (NTRS)

Georgiadis, Nicholas J.; Rumsey, Christopher L.; Huang, George P.

2015-01-01

Two axisymmetric shock-wave/boundary-layer interaction (SWBLI) cases are used to benchmark one- and two-equation Reynolds-averaged Navier-Stokes (RANS) turbulence models. This validation exercise was executed in the philosophy of the NASA Turbulence Modeling Resource and the AIAA Turbulence Model Benchmarking Working Group. Both SWBLI cases are from the experiments of Kussoy and Horstman for axisymmetric compression corner geometries with SWBLI inducing flares of 20 and 30 degrees, respectively. The freestream Mach number was approximately 7. The RANS closures examined are the Spalart-Allmaras one-equation model and the Menter family of kappa - omega two equation models including the Baseline and Shear Stress Transport formulations. The Wind-US and CFL3D RANS solvers are employed to simulate the SWBLI cases. Comparisons of RANS solutions to experimental data are made for a boundary layer survey plane just upstream of the SWBLI region. In the SWBLI region, comparisons of surface pressure and heat transfer are made. The effects of inflow modeling strategy, grid resolution, grid orthogonality, turbulent Prandtl number, and code-to-code variations are also addressed.

Capacity improvement using simulation optimization approaches: A case study in the thermotechnology industry

NASA Astrophysics Data System (ADS)

Yelkenci Köse, Simge; Demir, Leyla; Tunalı, Semra; Türsel Eliiyi, Deniz

2015-02-01

In manufacturing systems, optimal buffer allocation has a considerable impact on capacity improvement. This study presents a simulation optimization procedure to solve the buffer allocation problem in a heat exchanger production plant so as to improve the capacity of the system. For optimization, three metaheuristic-based search algorithms, i.e. a binary-genetic algorithm (B-GA), a binary-simulated annealing algorithm (B-SA) and a binary-tabu search algorithm (B-TS), are proposed. These algorithms are integrated with the simulation model of the production line. The simulation model, which captures the stochastic and dynamic nature of the production line, is used as an evaluation function for the proposed metaheuristics. The experimental study with benchmark problem instances from the literature and the real-life problem show that the proposed B-TS algorithm outperforms B-GA and B-SA in terms of solution quality.

A suite of exercises for verifying dynamic earthquake rupture codes

USGS Publications Warehouse

Harris, Ruth A.; Barall, Michael; Aagaard, Brad T.; Ma, Shuo; Roten, Daniel; Olsen, Kim B.; Duan, Benchun; Liu, Dunyu; Luo, Bin; Bai, Kangchen; Ampuero, Jean-Paul; Kaneko, Yoshihiro; Gabriel, Alice-Agnes; Duru, Kenneth; Ulrich, Thomas; Wollherr, Stephanie; Shi, Zheqiang; Dunham, Eric; Bydlon, Sam; Zhang, Zhenguo; Chen, Xiaofei; Somala, Surendra N.; Pelties, Christian; Tago, Josue; Cruz-Atienza, Victor Manuel; Kozdon, Jeremy; Daub, Eric; Aslam, Khurram; Kase, Yuko; Withers, Kyle; Dalguer, Luis

2018-01-01

We describe a set of benchmark exercises that are designed to test if computer codes that simulate dynamic earthquake rupture are working as intended. These types of computer codes are often used to understand how earthquakes operate, and they produce simulation results that include earthquake size, amounts of fault slip, and the patterns of ground shaking and crustal deformation. The benchmark exercises examine a range of features that scientists incorporate in their dynamic earthquake rupture simulations. These include implementations of simple or complex fault geometry, off‐fault rock response to an earthquake, stress conditions, and a variety of formulations for fault friction. Many of the benchmarks were designed to investigate scientific problems at the forefronts of earthquake physics and strong ground motions research. The exercises are freely available on our website for use by the scientific community.

Estimation of an optimal chemotherapy utilisation rate for cancer: setting an evidence-based benchmark for quality cancer care.

PubMed

Jacob, S A; Ng, W L; Do, V

2015-02-01

There is wide variation in the proportion of newly diagnosed cancer patients who receive chemotherapy, indicating the need for a benchmark rate of chemotherapy utilisation. This study describes an evidence-based model that estimates the proportion of new cancer patients in whom chemotherapy is indicated at least once (defined as the optimal chemotherapy utilisation rate). The optimal chemotherapy utilisation rate can act as a benchmark for measuring and improving the quality of care. Models of optimal chemotherapy utilisation were constructed for each cancer site based on indications for chemotherapy identified from evidence-based treatment guidelines. Data on the proportion of patient- and tumour-related attributes for which chemotherapy was indicated were obtained, using population-based data where possible. Treatment indications and epidemiological data were merged to calculate the optimal chemotherapy utilisation rate. Monte Carlo simulations and sensitivity analyses were used to assess the effect of controversial chemotherapy indications and variations in epidemiological data on our model. Chemotherapy is indicated at least once in 49.1% (95% confidence interval 48.8-49.6%) of all new cancer patients in Australia. The optimal chemotherapy utilisation rates for individual tumour sites ranged from a low of 13% in thyroid cancers to a high of 94% in myeloma. The optimal chemotherapy utilisation rate can serve as a benchmark for planning chemotherapy services on a population basis. The model can be used to evaluate service delivery by comparing the benchmark rate with patterns of care data. The overall estimate for other countries can be obtained by substituting the relevant distribution of cancer types. It can also be used to predict future chemotherapy workload and can be easily modified to take into account future changes in cancer incidence, presentation stage or chemotherapy indications. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Mapping the Martian Meteorology

NASA Technical Reports Server (NTRS)

Allison, M.; Ross, J. D.; Solomon, N.

1999-01-01

The Mars-adapted version of the NASA/GISS general circulation model (GCM) has been applied to the hourly/daily simulation of the planet's meteorology over several seasonal orbits. The current running version of the model includes a diurnal solar cycle, CO2 sublimation, and a mature parameterization of upper level wave drag with a vertical domain extending from the surface up to the 6microb level. The benchmark simulations provide a four-dimensional archive for the comparative evaluation of various schemes for the retrieval of winds from anticipated polar orbiter measurements of temperatures by the Pressure Modulator Infrared Radiometer. Additional information is contained in the original extended abstract.

Learning in Stochastic Bit Stream Neural Networks.

PubMed

van Daalen, Max; Shawe-Taylor, John; Zhao, Jieyu

1996-08-01

This paper presents learning techniques for a novel feedforward stochastic neural network. The model uses stochastic weights and the "bit stream" data representation. It has a clean analysable functionality and is very attractive with its great potential to be implemented in hardware using standard digital VLSI technology. The design allows simulation at three different levels and learning techniques are described for each level. The lowest level corresponds to on-chip learning. Simulation results on three benchmark MONK's problems and handwritten digit recognition with a clean set of 500 16 x 16 pixel digits demonstrate that the new model is powerful enough for the real world applications. Copyright 1996 Elsevier Science Ltd

Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model.

PubMed

Jämbeck, Joakim P M; Eriksson, Emma S E; Laaksonen, Aatto; Lyubartsev, Alexander P; Eriksson, Leif A

2014-01-14

Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous "droplet" through the liposome bilayer are reported herein.

A neurally plausible parallel distributed processing model of event-related potential word reading data.

PubMed

Laszlo, Sarah; Plaut, David C

2012-03-01

The Parallel Distributed Processing (PDP) framework has significant potential for producing models of cognitive tasks that approximate how the brain performs the same tasks. To date, however, there has been relatively little contact between PDP modeling and data from cognitive neuroscience. In an attempt to advance the relationship between explicit, computational models and physiological data collected during the performance of cognitive tasks, we developed a PDP model of visual word recognition which simulates key results from the ERP reading literature, while simultaneously being able to successfully perform lexical decision-a benchmark task for reading models. Simulations reveal that the model's success depends on the implementation of several neurally plausible features in its architecture which are sufficiently domain-general to be relevant to cognitive modeling more generally. Copyright © 2011 Elsevier Inc. All rights reserved.

A geographic information system-based 3D city estate modeling and simulation system

NASA Astrophysics Data System (ADS)

Chong, Xiaoli; Li, Sha

2015-12-01

This paper introduces a 3D city simulation system which is based on geographic information system (GIS), covering all commercial housings of the city. A regional- scale, GIS-based approach is used to capture, describe, and track the geographical attributes of each house in the city. A sorting algorithm of "Benchmark + Parity Rate" is developed to cluster houses with similar spatial and construction attributes. This system is applicable for digital city modeling, city planning, housing evaluation, housing monitoring, and visualizing housing transaction. Finally, taking Jingtian area of Shenzhen as an example, the each unit of 35,997 houses in the area could be displayed, tagged, and easily tracked by the GIS-based city modeling and simulation system. The match market real conditions well and can be provided to house buyers as reference.

The development of a virtual reality training curriculum for colonoscopy.

PubMed

Sugden, Colin; Aggarwal, Rajesh; Banerjee, Amrita; Haycock, Adam; Thomas-Gibson, Siwan; Williams, Christopher B; Darzi, Ara

2012-07-01

The development of a structured virtual reality (VR) training curriculum for colonoscopy using high-fidelity simulation. Colonoscopy requires detailed knowledge and technical skill. Changes to working practices in recent times have reduced the availability of traditional training opportunities. Much might, therefore, be achieved by applying novel technologies such as VR simulation to colonoscopy. Scientifically developed device-specific curricula aim to maximize the yield of laboratory-based training by focusing on validated modules and linking progression to the attainment of benchmarked proficiency criteria. Fifty participants comprised of 30 novices (<10 colonoscopies), 10 intermediates (100 to 500 colonoscopies), and 10 experienced (>500 colonoscopies) colonoscopists were recruited to participate. Surrogates of proficiency, such as number of procedures undertaken, determined prospective allocation to 1 of 3 groups (novice, intermediate, and experienced). Construct validity and learning value (comparison between groups and within groups respectively) for each task and metric on the chosen simulator model determined suitability for inclusion in the curriculum. Eight tasks in possession of construct validity and significant learning curves were included in the curriculum: 3 abstract tasks, 4 part-procedural tasks, and 1 procedural task. The whole-procedure task was valid for 11 metrics including the following: "time taken to complete the task" (1238, 343, and 293 s; P < 0.001) and "insertion length with embedded tip" (23.8, 3.6, and 4.9 cm; P = 0.005). Learning curves consistently plateaued at or beyond the ninth attempt. Valid metrics were used to define benchmarks, derived from the performance of the experienced cohort, for each included task. A comprehensive, stratified, benchmarked, whole-procedure curriculum has been developed for a modern high-fidelity VR colonoscopy simulator.

Accurate Mapping of Multilevel Rydberg Atoms on Interacting Spin-1 /2 Particles for the Quantum Simulation of Ising Models

NASA Astrophysics Data System (ADS)

de Léséleuc, Sylvain; Weber, Sebastian; Lienhard, Vincent; Barredo, Daniel; Büchler, Hans Peter; Lahaye, Thierry; Browaeys, Antoine

2018-03-01

We study a system of atoms that are laser driven to n D3 /2 Rydberg states and assess how accurately they can be mapped onto spin-1 /2 particles for the quantum simulation of anisotropic Ising magnets. Using nonperturbative calculations of the pair potentials between two atoms in the presence of electric and magnetic fields, we emphasize the importance of a careful selection of experimental parameters in order to maintain the Rydberg blockade and avoid excitation of unwanted Rydberg states. We benchmark these theoretical observations against experiments using two atoms. Finally, we show that in these conditions, the experimental dynamics observed after a quench is in good agreement with numerical simulations of spin-1 /2 Ising models in systems with up to 49 spins, for which numerical simulations become intractable.

Benchmark Data Set for Wheat Growth Models: Field Experiments and AgMIP Multi-Model Simulations.

NASA Technical Reports Server (NTRS)

Asseng, S.; Ewert, F.; Martre, P.; Rosenzweig, C.; Jones, J. W.; Hatfield, J. L.; Ruane, A. C.; Boote, K. J.; Thorburn, P.J.; Rotter, R. P.

2015-01-01

The data set includes a current representative management treatment from detailed, quality-tested sentinel field experiments with wheat from four contrasting environments including Australia, The Netherlands, India and Argentina. Measurements include local daily climate data (solar radiation, maximum and minimum temperature, precipitation, surface wind, dew point temperature, relative humidity, and vapor pressure), soil characteristics, frequent growth, nitrogen in crop and soil, crop and soil water and yield components. Simulations include results from 27 wheat models and a sensitivity analysis with 26 models and 30 years (1981-2010) for each location, for elevated atmospheric CO2 and temperature changes, a heat stress sensitivity analysis at anthesis, and a sensitivity analysis with soil and crop management variations and a Global Climate Model end-century scenario.

CHIC - Coupling Habitability, Interior and Crust

NASA Astrophysics Data System (ADS)

Noack, Lena; Labbe, Francois; Boiveau, Thomas; Rivoldini, Attilio; Van Hoolst, Tim

2014-05-01

We present a new code developed for simulating convection in terrestrial planets and icy moons. The code CHIC is written in Fortran and employs the finite volume method and finite difference method for solving energy, mass and momentum equations in either silicate or icy mantles. The code uses either Cartesian (2D and 3D box) or spherical coordinates (2D cylinder or annulus). It furthermore contains a 1D parametrised model to obtain temperature profiles in specific regions, for example in the iron core or in the silicate mantle (solving only the energy equation). The 2D/3D convection model uses the same input parameters as the 1D model, which allows for comparison of the different models and adaptation of the 1D model, if needed. The code has already been benchmarked for the following aspects: - viscosity-dependent rheology (Blankenbach et al., 1989) - pseudo-plastic deformation (Tosi et al., in preparation phase) - subduction mechanism and plastic deformation (Quinquis et al., in preparation phase) New features that are currently developed and benchmarked include: - compressibility (following King et al., 2009 and Leng and Zhong, 2008) - different melt modules (Plesa et al., in preparation phase) - freezing of an inner core (comparison with GAIA code, Huettig and Stemmer, 2008) - build-up of oceanic and continental crust (Noack et al., in preparation phase) The code represents a useful tool to couple the interior with the surface of a planet (e.g. via build-up and erosion of crust) and it's atmosphere (via outgassing on the one hand and subduction of hydrated crust and carbonates back into the mantle). It will be applied to investigate several factors that might influence the habitability of a terrestrial planet, and will also be used to simulate icy bodies with high-pressure ice phases. References: Blankenbach et al. (1989). A benchmark comparison for mantle convection codes. GJI 98, 23-38. Huettig and Stemmer (2008). Finite volume discretization for dynamic viscosities on Voronoi grids. PEPI 171(1-4), 137-146. King et al. (2009). A Community Benchmark for 2D Cartesian Compressible Convection in the Earth's Mantle. GJI 179, 1-11. Leng and Zhong (2008). Viscous heating, adiabatic heating and energetic consistency in compressible mantle convection. GJI 173, 693-702.

Benchmark Modeling of the Near-Field and Far-Field Wave Effects of Wave Energy Arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rhinefrank, Kenneth E; Haller, Merrick C; Ozkan-Haller, H Tuba

2013-01-26

This project is an industry-led partnership between Columbia Power Technologies and Oregon State University that will perform benchmark laboratory experiments and numerical modeling of the near-field and far-field impacts of wave scattering from an array of wave energy devices. These benchmark experimental observations will help to fill a gaping hole in our present knowledge of the near-field effects of multiple, floating wave energy converters and are a critical requirement for estimating the potential far-field environmental effects of wave energy arrays. The experiments will be performed at the Hinsdale Wave Research Laboratory (Oregon State University) and will utilize an array ofmore » newly developed Buoys' that are realistic, lab-scale floating power converters. The array of Buoys will be subjected to realistic, directional wave forcing (1:33 scale) that will approximate the expected conditions (waves and water depths) to be found off the Central Oregon Coast. Experimental observations will include comprehensive in-situ wave and current measurements as well as a suite of novel optical measurements. These new optical capabilities will include imaging of the 3D wave scattering using a binocular stereo camera system, as well as 3D device motion tracking using a newly acquired LED system. These observing systems will capture the 3D motion history of individual Buoys as well as resolve the 3D scattered wave field; thus resolving the constructive and destructive wave interference patterns produced by the array at high resolution. These data combined with the device motion tracking will provide necessary information for array design in order to balance array performance with the mitigation of far-field impacts. As a benchmark data set, these data will be an important resource for testing of models for wave/buoy interactions, buoy performance, and far-field effects on wave and current patterns due to the presence of arrays. Under the proposed project we will initiate high-resolution (fine scale, very near-field) fluid/structure interaction simulations of buoy motions, as well as array-scale, phase-resolving wave scattering simulations. These modeling efforts will utilize state-of-the-art research quality models, which have not yet been brought to bear on this complex problem of large array wave/structure interaction problem.« less

Efficiently passing messages in distributed spiking neural network simulation.

PubMed

Thibeault, Corey M; Minkovich, Kirill; O'Brien, Michael J; Harris, Frederick C; Srinivasa, Narayan

2013-01-01

Efficiently passing spiking messages in a neural model is an important aspect of high-performance simulation. As the scale of networks has increased so has the size of the computing systems required to simulate them. In addition, the information exchange of these resources has become more of an impediment to performance. In this paper we explore spike message passing using different mechanisms provided by the Message Passing Interface (MPI). A specific implementation, MVAPICH, designed for high-performance clusters with Infiniband hardware is employed. The focus is on providing information about these mechanisms for users of commodity high-performance spiking simulators. In addition, a novel hybrid method for spike exchange was implemented and benchmarked.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated onmore » three benchmarking systems, with special focus on approximation accuracy and efficiency.« less

Performance of Multi-chaotic PSO on a shifted benchmark functions set

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pluhacek, Michal; Senkerik, Roman; Zelinka, Ivan

2015-03-10

In this paper the performance of Multi-chaotic PSO algorithm is investigated using two shifted benchmark functions. The purpose of shifted benchmark functions is to simulate the time-variant real-world problems. The results of chaotic PSO are compared with canonical version of the algorithm. It is concluded that using the multi-chaotic approach can lead to better results in optimization of shifted functions.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

PubMed

Ó Conchúir, Shane; Barlow, Kyle A; Pache, Roland A; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J; Smith, Colin A; Kortemme, Tanja

2015-01-01

The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

a Proposed Benchmark Problem for Scatter Calculations in Radiographic Modelling

NASA Astrophysics Data System (ADS)

Jaenisch, G.-R.; Bellon, C.; Schumm, A.; Tabary, J.; Duvauchelle, Ph.

2009-03-01

Code Validation is a permanent concern in computer modelling, and has been addressed repeatedly in eddy current and ultrasonic modeling. A good benchmark problem is sufficiently simple to be taken into account by various codes without strong requirements on geometry representation capabilities, focuses on few or even a single aspect of the problem at hand to facilitate interpretation and to avoid that compound errors compensate themselves, yields a quantitative result and is experimentally accessible. In this paper we attempt to address code validation for one aspect of radiographic modeling, the scattered radiation prediction. Many NDT applications can not neglect scattered radiation, and the scatter calculation thus is important to faithfully simulate the inspection situation. Our benchmark problem covers the wall thickness range of 10 to 50 mm for single wall inspections, with energies ranging from 100 to 500 keV in the first stage, and up to 1 MeV with wall thicknesses up to 70 mm in the extended stage. A simple plate geometry is sufficient for this purpose, and the scatter data is compared on a photon level, without a film model, which allows for comparisons with reference codes like MCNP. We compare results of three Monte Carlo codes (McRay, Sindbad and Moderato) as well as an analytical first order scattering code (VXI), and confront them to results obtained with MCNP. The comparison with an analytical scatter model provides insights into the application domain where this kind of approach can successfully replace Monte-Carlo calculations.

An End-to-End simulator for the development of atmospheric corrections and temperature - emissivity separation algorithms in the TIR spectral domain

NASA Astrophysics Data System (ADS)

Rock, Gilles; Fischer, Kim; Schlerf, Martin; Gerhards, Max; Udelhoven, Thomas

2017-04-01

The development and optimization of image processing algorithms requires the availability of datasets depicting every step from earth surface to the sensor's detector. The lack of ground truth data obliges to develop algorithms on simulated data. The simulation of hyperspectral remote sensing data is a useful tool for a variety of tasks such as the design of systems, the understanding of the image formation process, and the development and validation of data processing algorithms. An end-to-end simulator has been set up consisting of a forward simulator, a backward simulator and a validation module. The forward simulator derives radiance datasets based on laboratory sample spectra, applies atmospheric contributions using radiative transfer equations, and simulates the instrument response using configurable sensor models. This is followed by the backward simulation branch, consisting of an atmospheric correction (AC), a temperature and emissivity separation (TES) or a hybrid AC and TES algorithm. An independent validation module allows the comparison between input and output dataset and the benchmarking of different processing algorithms. In this study, hyperspectral thermal infrared scenes of a variety of surfaces have been simulated to analyze existing AC and TES algorithms. The ARTEMISS algorithm was optimized and benchmarked against the original implementations. The errors in TES were found to be related to incorrect water vapor retrieval. The atmospheric characterization could be optimized resulting in increasing accuracies in temperature and emissivity retrieval. Airborne datasets of different spectral resolutions were simulated from terrestrial HyperCam-LW measurements. The simulated airborne radiance spectra were subjected to atmospheric correction and TES and further used for a plant species classification study analyzing effects related to noise and mixed pixels.

Simulations of hypervelocity impacts for asteroid deflection studies

NASA Astrophysics Data System (ADS)

Heberling, T.; Ferguson, J. M.; Gisler, G. R.; Plesko, C. S.; Weaver, R.

2016-12-01

The possibility of kinetic-impact deflection of threatening near-earth asteroids will be tested for the first time in the proposed AIDA (Asteroid Impact Deflection Assessment) mission, involving two independent spacecraft, NASAs DART (Double Asteroid Redirection Test) and ESAs AIM (Asteroid Impact Mission). The impact of the DART spacecraft onto the secondary of the binary asteroid 65803 Didymos, at a speed of 5 to 7 km/s, is expected to alter the mutual orbit by an observable amount. The velocity imparted to the secondary depends on the geometry and dynamics of the impact, and especially on the momentum enhancement factor, conventionally called beta. We use the Los Alamos hydrocodes Rage and Pagosa to estimate beta in laboratory-scale benchmark experiments and in the large-scale asteroid deflection test. Simulations are performed in two- and three-dimensions, using a variety of equations of state and strength models for both the lab-scale and large-scale cases. This work is being performed as part of a systematic benchmarking study for the AIDA mission that includes other hydrocodes.

A High Performance Computing Framework for Physics-based Modeling and Simulation of Military Ground Vehicles

DTIC Science & Technology

2011-03-25

number one and Nebulae at number three. Both systems rely on GPU co-processing and use Intel Xeon processors cards and NVIDIA Tesla C2050 GPUs. In...spite of a theoretical peak capability of almost 3 Petaflop/s, Nebulae clocked at 1.271 PFlop/s when running the Linpack benchmark, which puts it

Generating Shifting Workloads to Benchmark Adaptability in Relational Database Systems

NASA Astrophysics Data System (ADS)

Rabl, Tilmann; Lang, Andreas; Hackl, Thomas; Sick, Bernhard; Kosch, Harald

A large body of research concerns the adaptability of database systems. Many commercial systems already contain autonomic processes that adapt configurations as well as data structures and data organization. Yet there is virtually no possibility for a just measurement of the quality of such optimizations. While standard benchmarks have been developed that simulate real-world database applications very precisely, none of them considers variations in workloads produced by human factors. Today’s benchmarks test the performance of database systems by measuring peak performance on homogeneous request streams. Nevertheless, in systems with user interaction access patterns are constantly shifting. We present a benchmark that simulates a web information system with interaction of large user groups. It is based on the analysis of a real online eLearning management system with 15,000 users. The benchmark considers the temporal dependency of user interaction. Main focus is to measure the adaptability of a database management system according to shifting workloads. We will give details on our design approach that uses sophisticated pattern analysis and data mining techniques.

Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

2016-02-01

We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

Numerical simulation of the submarine landslides and tsunami occurred at Port Valdez, AK during 1964 Alaska Earthquake with Landslide-HySEA model

NASA Astrophysics Data System (ADS)

González-Vida, Jose M.; Ortega, Sergio; Macías, Jorge; Castro, Manuel J.; Escalante, Cipriano

2017-04-01

This is a benchmark problem recently proposed in the framework of the Landslide Tsunami Model Benchmarking Workshop organized by the NTHMP (National tsunami Hazard mitigation program -USA-) at Galveston (USA). The benchmark is based on the historical event which occurred at Port Valdez, AK during the Alaska Earthquake of March 27, 1964. The great disaster during the Mw9.2 Alaska Earthquake happened in the dock and harbour area of Port Valdez, where a massive submarine landslide generated a tsunami, inundating the waterfront up to two blocks inland. Then, a second wave crossed the waterfront 10-15 minutes after the first wave, carrying a large amount of the debris. It has been described as a violent surging wave only slightly smaller than the first. It is believed that the second wave which flooded the waterfront was originated at the other side of the Port Valdez near the Shoup Bay moraine. The benchmark consists in simulating with the (GPU based) Landslide-HySEA model the extent of inundation for two slide events, based on before and after bathymetry data, eye-witness observations of the event, and observed runup distribution. First, both landslides have been simulated separately, studying time series of the water waves at determined locations, runups at different areas and the extent of inundation around the first two blocks inland of Port Valdez. Then, the two landslides are triggered at the same time and the joint effect is studied. Obtained results are satisfactory and they agree with the existing observations. References Castro, M. J., Fernández-Nieto, E. D., González-Vida, J. M., Parés, C. (2011). Numerical Treatment of the Loss of Hyperbolicity of the Two-Layer Shallow-Water System. Journal of Scientific Computing, 48(1):16-40. Fernández, E.H., Bouchut, F., Bresh, D., Castro, M.J. and, Mangeney, A. (2008). A new Savage-Hutter type model for submarine avalanches and generated tsunami. J. Comp. Phys., 227: 7720-7754. Fernández-Nieto, E.D., Castro, M.J., Parés, C. (2011). On an Intermediate Field Capturing Riemann Solver Based on a Parabolic Viscosity Matrix for the Two-Layer Shallow Water System. J. Sci. Comp. 48:117-140. Macías, J., Vázquez, J.T., Fernández-Salas, L.M., González-Vida, J.M., Bárcenas, P., Castro, M.J., Díaz-del-Río, and V., Alonso, B. (2015). The Al-Boraní submarine landslide and associated tsunami. A modelling approach. Marine Geology, 361:79-95.

High Frequency Bottom Interaction in Range Dependent Biot Media

DTIC Science & Technology

1999-09-30

acoust . Soc. Am. Stephen, R.A. Benchmark models for propagation and scattering in Biot media. Fall ASA, Norfolk, VA, October...1998, J. Acoust . Soc. Am., 104, 1808. X. Zhu and G. A. McMechan, “Numerical simulation of seismic responses of poroelastic reservoirs using Biot...reverberation from rough and heterogeneous seafloors. J. acoust . Soc. Am. Stephen, R.A., in press. Optimum and standard beam widths for numerical modeling of interface scattering problems. J. acoust . Soc. Am.

Earth-Abundant Materials as Photosensitizers in the Molecular Assemblies for Solar Energy Conversion

DTIC Science & Technology

2013-03-31

experimentally by several research groups ,3-8   which provide us with a starting point and a set of benchmarks for our theoretical calculations. In this...binding mode. All the nonequivalent linker positions on the dyes were modeled: two nonequivalent carboxylic acid groups on 1 and 2 and two... nonequivalent cyanide groups on 3. All optimizations were performed in vacuum. Interfacial Electron Transfer Simulations. All model systems were composed of a

Time-Dependent Simulations of Incompressible Flow in a Turbopump Using Overset Grid Approach

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan

2001-01-01

This viewgraph presentation provides information on mathematical modelling of the SSME (space shuttle main engine). The unsteady SSME-rig1 start-up procedure from the pump at rest has been initiated by using 34.3 million grid points. The computational model for the SSME-rig1 has been completed. Moving boundary capability is obtained by using DCF module in OVERFLOW-D. MPI (Message Passing Interface)/OpenMP hybrid parallel code has been benchmarked.

Modelling of a Solar Thermal Power Plant for Benchmarking Blackbox Optimization Solvers

NASA Astrophysics Data System (ADS)

Lemyre Garneau, Mathieu

A new family of problems is provided to serve as a benchmark for blackbox optimization solvers. The problems are single or bi-objective and vary in complexity in terms of the number of variables used (from 5 to 29), the type of variables (integer, real, category), the number of constraints (from 5 to 17) and their types (binary or continuous). In order to provide problems exhibiting dynamics that reflect real engineering challenges, they are extracted from an original numerical model of a concentrated solar power (CSP) power plant with molten salt thermal storage. The model simulates the performance of the power plant by using a high level modeling of each of its main components, namely, an heliostats field, a central cavity receiver, a molten salt heat storage, a steam generator and an idealized powerblock. The heliostats field layout is determined through a simple automatic strategy that finds the best individual positions on the field by considering their respective cosine efficiency, atmospheric scattering and spillage losses as a function of the design parameters. A Monte-Carlo integral method is used to evaluate the heliostats field's optical performance throughout the day so that shadowing effects between heliostats are considered, and the results of this evaluation provide the inputs to simulate the levels and temperatures of the thermal storage. The molten salt storage inventory is used to transfer thermal energy to the powerblock, which simulates a simple Rankine cycle with a single steam turbine. Auxiliary models are used to provide additional optimization constraints on the investment cost, parasitic losses or components failure. The results of preliminary optimizations performed with the NOMAD software using default settings are provided to show the validity of the problems.

Plasma Modeling with Speed-Limited Particle-in-Cell Techniques

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Werner, G. R.; Cary, J. R.; Stoltz, P. H.

2017-10-01

Speed-limited particle-in-cell (SLPIC) modeling is a new particle simulation technique for modeling systems wherein numerical constraints, e.g. limitations on timestep size required for numerical stability, are significantly more restrictive than is needed to model slower kinetic processes of interest. SLPIC imposes artificial speed-limiting behavior on fast particles whose kinetics do not play meaningful roles in the system dynamics, thus enabling larger simulation timesteps and more rapid modeling of such plasma discharges. The use of SLPIC methods to model plasma sheath formation and the free expansion of plasma into vacuum will be demonstrated. Wallclock times for these simulations, relative to conventional PIC, are reduced by a factor of 2.5 for the plasma expansion problem and by over 6 for the sheath formation problem; additional speedup is likely possible. Physical quantities of interest are shown to be correct for these benchmark problems. Additional SLPIC applications will also be discussed. Supported by US DoE SBIR Phase I/II Award DE-SC0015762.

An analytical benchmark and a Mathematica program for MD codes: Testing LAMMPS on the 2nd generation Brenner potential

NASA Astrophysics Data System (ADS)

Favata, Antonino; Micheletti, Andrea; Ryu, Seunghwa; Pugno, Nicola M.

2016-10-01

An analytical benchmark and a simple consistent Mathematica program are proposed for graphene and carbon nanotubes, that may serve to test any molecular dynamics code implemented with REBO potentials. By exploiting the benchmark, we checked results produced by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) when adopting the second generation Brenner potential, we made evident that this code in its current implementation produces results which are offset from those of the benchmark by a significant amount, and provide evidence of the reason.

Experimental benchmarking of a Monte Carlo dose simulation code for pediatric CT

NASA Astrophysics Data System (ADS)

Li, Xiang; Samei, Ehsan; Yoshizumi, Terry; Colsher, James G.; Jones, Robert P.; Frush, Donald P.

2007-03-01

In recent years, there has been a desire to reduce CT radiation dose to children because of their susceptibility and prolonged risk for cancer induction. Concerns arise, however, as to the impact of dose reduction on image quality and thus potentially on diagnostic accuracy. To study the dose and image quality relationship, we are developing a simulation code to calculate organ dose in pediatric CT patients. To benchmark this code, a cylindrical phantom was built to represent a pediatric torso, which allows measurements of dose distributions from its center to its periphery. Dose distributions for axial CT scans were measured on a 64-slice multidetector CT (MDCT) scanner (GE Healthcare, Chalfont St. Giles, UK). The same measurements were simulated using a Monte Carlo code (PENELOPE, Universitat de Barcelona) with the applicable CT geometry including bowtie filter. The deviations between simulated and measured dose values were generally within 5%. To our knowledge, this work is one of the first attempts to compare measured radial dose distributions on a cylindrical phantom with Monte Carlo simulated results. It provides a simple and effective method for benchmarking organ dose simulation codes and demonstrates the potential of Monte Carlo simulation for investigating the relationship between dose and image quality for pediatric CT patients.

Science based integrated approach to advanced nuclear fuel development - integrated multi-scale multi-physics hierarchical modeling and simulation framework Part III: cladding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tome, Carlos N; Caro, J A; Lebensohn, R A

2010-01-01

Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Reactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems to develop predictive tools is critical. Not only are fabrication and performance models needed to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating themore » phase and microstructural behavior of the nuclear fuel system materials and matrices. In this paper we review the current status of the advanced modeling and simulation of nuclear reactor cladding, with emphasis on what is available and what is to be developed in each scale of the project, how we propose to pass information from one scale to the next, and what experimental information is required for benchmarking and advancing the modeling at each scale level.« less

Numerical simulation on hydromechanical coupling in porous media adopting three-dimensional pore-scale model.

PubMed

Liu, Jianjun; Song, Rui; Cui, Mengmeng

2014-01-01

A novel approach of simulating hydromechanical coupling in pore-scale models of porous media is presented in this paper. Parameters of the sandstone samples, such as the stress-strain curve, Poisson's ratio, and permeability under different pore pressure and confining pressure, are tested in laboratory scale. The micro-CT scanner is employed to scan the samples for three-dimensional images, as input to construct the model. Accordingly, four physical models possessing the same pore and rock matrix characteristics as the natural sandstones are developed. Based on the micro-CT images, the three-dimensional finite element models of both rock matrix and pore space are established by MIMICS and ICEM software platform. Navier-Stokes equation and elastic constitutive equation are used as the mathematical model for simulation. A hydromechanical coupling analysis in pore-scale finite element model of porous media is simulated by ANSYS and CFX software. Hereby, permeability of sandstone samples under different pore pressure and confining pressure has been predicted. The simulation results agree well with the benchmark data. Through reproducing its stress state underground, the prediction accuracy of the porous rock permeability in pore-scale simulation is promoted. Consequently, the effects of pore pressure and confining pressure on permeability are revealed from the microscopic view.

Numerical Simulation on Hydromechanical Coupling in Porous Media Adopting Three-Dimensional Pore-Scale Model

PubMed Central

Liu, Jianjun; Song, Rui; Cui, Mengmeng

2014-01-01

A novel approach of simulating hydromechanical coupling in pore-scale models of porous media is presented in this paper. Parameters of the sandstone samples, such as the stress-strain curve, Poisson's ratio, and permeability under different pore pressure and confining pressure, are tested in laboratory scale. The micro-CT scanner is employed to scan the samples for three-dimensional images, as input to construct the model. Accordingly, four physical models possessing the same pore and rock matrix characteristics as the natural sandstones are developed. Based on the micro-CT images, the three-dimensional finite element models of both rock matrix and pore space are established by MIMICS and ICEM software platform. Navier-Stokes equation and elastic constitutive equation are used as the mathematical model for simulation. A hydromechanical coupling analysis in pore-scale finite element model of porous media is simulated by ANSYS and CFX software. Hereby, permeability of sandstone samples under different pore pressure and confining pressure has been predicted. The simulation results agree well with the benchmark data. Through reproducing its stress state underground, the prediction accuracy of the porous rock permeability in pore-scale simulation is promoted. Consequently, the effects of pore pressure and confining pressure on permeability are revealed from the microscopic view. PMID:24955384

Wang-Landau method for calculating Rényi entropies in finite-temperature quantum Monte Carlo simulations.

PubMed

Inglis, Stephen; Melko, Roger G

2013-01-01

We implement a Wang-Landau sampling technique in quantum Monte Carlo (QMC) simulations for the purpose of calculating the Rényi entanglement entropies and associated mutual information. The algorithm converges an estimate for an analog to the density of states for stochastic series expansion QMC, allowing a direct calculation of Rényi entropies without explicit thermodynamic integration. We benchmark results for the mutual information on two-dimensional (2D) isotropic and anisotropic Heisenberg models, a 2D transverse field Ising model, and a three-dimensional Heisenberg model, confirming a critical scaling of the mutual information in cases with a finite-temperature transition. We discuss the benefits and limitations of broad sampling techniques compared to standard importance sampling methods.

High Fidelity BWR Fuel Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Su Jong

This report describes the Consortium for Advanced Simulation of Light Water Reactors (CASL) work conducted for completion of the Thermal Hydraulics Methods (THM) Level 3 milestone THM.CFD.P13.03: High Fidelity BWR Fuel Simulation. High fidelity computational fluid dynamics (CFD) simulation for Boiling Water Reactor (BWR) was conducted to investigate the applicability and robustness performance of BWR closures. As a preliminary study, a CFD model with simplified Ferrule spacer grid geometry of NUPEC BWR Full-size Fine-mesh Bundle Test (BFBT) benchmark has been implemented. Performance of multiphase segregated solver with baseline boiling closures has been evaluated. Although the mean values of void fractionmore » and exit quality of CFD result for BFBT case 4101-61 agreed with experimental data, the local void distribution was not predicted accurately. The mesh quality was one of the critical factors to obtain converged result. The stability and robustness of the simulation was mainly affected by the mesh quality, combination of BWR closure models. In addition, the CFD modeling of fully-detailed spacer grid geometry with mixing vane is necessary for improving the accuracy of CFD simulation.« less

Benchmarking the evaluated proton differential cross sections suitable for the EBS analysis of natSi and 16O

NASA Astrophysics Data System (ADS)

Kokkoris, M.; Dede, S.; Kantre, K.; Lagoyannis, A.; Ntemou, E.; Paneta, V.; Preketes-Sigalas, K.; Provatas, G.; Vlastou, R.; Bogdanović-Radović, I.; Siketić, Z.; Obajdin, N.

2017-08-01

The evaluated proton differential cross sections suitable for the Elastic Backscattering Spectroscopy (EBS) analysis of natSi and 16O, as obtained from SigmaCalc 2.0, have been benchmarked over a wide energy and angular range at two different accelerator laboratories, namely at N.C.S.R. 'Demokritos', Athens, Greece and at Ruđer Bošković Institute (RBI), Zagreb, Croatia, using a variety of high-purity thick targets of known stoichiometry. The results are presented in graphical and tabular forms, while the observed discrepancies, as well as, the limits in accuracy of the benchmarking procedure, along with target related effects, are thoroughly discussed and analysed. In the case of oxygen the agreement between simulated and experimental spectra was generally good, while for silicon serious discrepancies were observed above Ep,lab = 2.5 MeV, suggesting that a further tuning of the appropriate nuclear model parameters in the evaluated differential cross-section datasets is required.

The particular use of PIV methods for the modelling of heat and hydrophysical processes in the nuclear power plants

NASA Astrophysics Data System (ADS)

Sergeev, D. A.; Kandaurov, A. A.; Troitskaya, Yu I.

2017-11-01

In this paper we describe PIV-system specially designed for the study of the hydrophysical processes in large-scale benchmark setup of promising fast reactor. The system allows the PIV-measurements for the conditions of complicated configuration of the reactor benchmark, reflections and distortions section of the laser sheet, blackout, in the closed volume. The use of filtering techniques and method of masks images enabled us to reduce the number of incorrect measurement of flow velocity vectors by an order. The method of conversion of image coordinates and velocity field in the reference model of the reactor using a virtual 3D simulation targets, without loss of accuracy in comparison with a method of using physical objects in filming area was released. The results of measurements of velocity fields in various modes, both stationary (workers), as well as in non-stationary (emergency).

Study of blood flow in several benchmark micro-channels using a two-fluid approach.

PubMed

Wu, Wei-Tao; Yang, Fang; Antaki, James F; Aubry, Nadine; Massoudi, Mehrdad

2015-10-01

It is known that in a vessel whose characteristic dimension (e.g., its diameter) is in the range of 20 to 500 microns, blood behaves as a non-Newtonian fluid, exhibiting complex phenomena, such as shear-thinning, stress relaxation, and also multi-component behaviors, such as the Fahraeus effect, plasma-skimming, etc. For describing these non-Newtonian and multi-component characteristics of blood, using the framework of mixture theory, a two-fluid model is applied, where the plasma is treated as a Newtonian fluid and the red blood cells (RBCs) are treated as shear-thinning fluid. A computational fluid dynamic (CFD) simulation incorporating the constitutive model was implemented using OpenFOAM® in which benchmark problems including a sudden expansion and various driven slots and crevices were studied numerically. The numerical results exhibited good agreement with the experimental observations with respect to both the velocity field and the volume fraction distribution of RBCs.

An Object-Oriented Serial DSMC Simulation Package

NASA Astrophysics Data System (ADS)

Liu, Hongli; Cai, Chunpei

2011-05-01

A newly developed three-dimensional direct simulation Monte Carlo (DSMC) simulation package, named GRASP ("Generalized Rarefied gAs Simulation Package"), is reported in this paper. This package utilizes the concept of simulation engine, many C++ features and software design patterns. The package has an open architecture which can benefit further development and maintenance of the code. In order to reduce the engineering time for three-dimensional models, a hybrid grid scheme, combined with a flexible data structure compiled by C++ language, are implemented in this package. This scheme utilizes a local data structure based on the computational cell to achieve high performance on workstation processors. This data structure allows the DSMC algorithm to be very efficiently parallelized with domain decomposition and it provides much flexibility in terms of grid types. This package can utilize traditional structured, unstructured or hybrid grids within the framework of a single code to model arbitrarily complex geometries and to simulate rarefied gas flows. Benchmark test cases indicate that this package has satisfactory accuracy for complex rarefied gas flows.

Allowing for Slow Evolution of Background Plasma in the 3D FDTD Plasma, Sheath, and Antenna Model

NASA Astrophysics Data System (ADS)

Smithe, David; Jenkins, Thomas; King, Jake

2015-11-01

We are working to include a slow-time evolution capability for what has previously been the static background plasma parameters, in the 3D finite-difference time-domain (FDTD) plasma and sheath model used to model ICRF antennas in fusion plasmas. A key aspect of this is SOL-density time-evolution driven by ponderomotive rarefaction from the strong fields in the vicinity of the antenna. We demonstrate and benchmark a Scalar Ponderomotive Potential method, based on local field amplitudes, which is included in the 3D simulation. And present a more advanced Tensor Ponderomotive Potential approach, which we hope to employ in the future, which should improve the physical fidelity in the highly anisotropic environment of the SOL. Finally, we demonstrate and benchmark slow time (non-linear) evolution of the RF sheath, and include realistic collisional effects from the neutral gas. Support from US DOE Grants DE-FC02-08ER54953, DE-FG02-09ER55006.

LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

PubMed Central

Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut

2008-01-01

Background Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms. Results We present LC-MSsim, a simulation software for LC-ESI-MS experiments. It simulates ESI spectra on the MS level. It reads a list of proteins from a FASTA file and digests the protein mixture using a user-defined enzyme. The software creates an LC-MS data set using a predictor for the retention time of the peptides and a model for peak shapes and elution profiles of the mass spectral peaks. Our software also offers the possibility to add contaminants, to change the background noise level and includes a model for the detectability of peptides in mass spectra. After the simulation, LC-MSsim writes the simulated data to mzData, a public XML format. The software also stores the positions (monoisotopic m/z and retention time) and ion counts of the simulated ions in separate files. Conclusion LC-MSsim generates simulated LC-MS data sets and incorporates models for peak shapes and contaminations. Algorithm developers can match the results of feature detection and alignment algorithms against the simulated ion lists and meaningful error rates can be computed. We anticipate that LC-MSsim will be useful to the wider community to perform benchmark studies and comparisons between computational tools. PMID:18842122

MCNP Simulation Benchmarks for a Portable Inspection System for Narcotics, Explosives, and Nuclear Material Detection

NASA Astrophysics Data System (ADS)

Alfonso, Krystal; Elsalim, Mashal; King, Michael; Strellis, Dan; Gozani, Tsahi

2013-04-01

MCNPX simulations have been used to guide the development of a portable inspection system for narcotics, explosives, and special nuclear material (SNM) detection. The system seeks to address these threats to national security by utilizing a high-yield, compact neutron source to actively interrogate the threats and produce characteristic signatures that can then be detected by radiation detectors. The portability of the system enables rapid deployment and proximity to threats concealed in small spaces. Both dD and dT electronic neutron generators (ENG) were used to interrogate ammonium nitrate fuel oil (ANFO) and cocaine hydrochloride, and the detector response of NaI, CsI, and LaBr3 were compared. The effect of tungsten shielding on the neutron flux in the gamma ray detectors was investigated, while carbon, beryllium, and polyethylene ENG moderator materials were optimized by determining the reaction rate density in the threats. In order to benchmark the modeling results, experimental measurements are compared with MCNPX simulations. In addition, the efficiency and die-away time of a portable differential die-away analysis (DDAA) detector using 3He proportional counters for SNM detection has been determined.

Gaming in risk-adjusted mortality rates: effect of misclassification of risk factors in the benchmarking of cardiac surgery risk-adjusted mortality rates.

PubMed

Siregar, Sabrina; Groenwold, Rolf H H; Versteegh, Michel I M; Noyez, Luc; ter Burg, Willem Jan P P; Bots, Michiel L; van der Graaf, Yolanda; van Herwerden, Lex A

2013-03-01

Upcoding or undercoding of risk factors could affect the benchmarking of risk-adjusted mortality rates. The aim was to investigate the effect of misclassification of risk factors on the benchmarking of mortality rates after cardiac surgery. A prospective cohort was used comprising all adult cardiac surgery patients in all 16 cardiothoracic centers in The Netherlands from January 1, 2007, to December 31, 2009. A random effects model, including the logistic European system for cardiac operative risk evaluation (EuroSCORE) was used to benchmark the in-hospital mortality rates. We simulated upcoding and undercoding of 5 selected variables in the patients from 1 center. These patients were selected randomly (nondifferential misclassification) or by the EuroSCORE (differential misclassification). In the random patients, substantial misclassification was required to affect benchmarking: a 1.8-fold increase in prevalence of the 4 risk factors changed an underperforming center into an average performing one. Upcoding of 1 variable required even more. When patients with the greatest EuroSCORE were upcoded (ie, differential misclassification), a 1.1-fold increase was sufficient: moderate left ventricular function from 14.2% to 15.7%, poor left ventricular function from 8.4% to 9.3%, recent myocardial infarction from 7.9% to 8.6%, and extracardiac arteriopathy from 9.0% to 9.8%. Benchmarking using risk-adjusted mortality rates can be manipulated by misclassification of the EuroSCORE risk factors. Misclassification of random patients or of single variables will have little effect. However, limited upcoding of multiple risk factors in high-risk patients can greatly influence benchmarking. To minimize "gaming," the prevalence of all risk factors should be carefully monitored. Copyright © 2013 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

Exploring tropical forest vegetation dynamics using the FATES model

NASA Astrophysics Data System (ADS)

Koven, C. D.; Fisher, R.; Knox, R. G.; Chambers, J.; Kueppers, L. M.; Christoffersen, B. O.; Davies, S. J.; Dietze, M.; Holm, J.; Massoud, E. C.; Muller-Landau, H. C.; Powell, T.; Serbin, S.; Shuman, J. K.; Walker, A. P.; Wright, S. J.; Xu, C.

2017-12-01

Tropical forest vegetation dynamics represent a critical climate feedback in the Earth system, which is poorly represented in current global modeling approaches. We discuss recent progress on exploring these dynamics using the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a demographic vegetation model for the CESM and ACME ESMs. We will discuss benchmarks of FATES predictions for forest structure against inventory sites, sensitivity of FATES predictions of size and age structure to model parameter uncertainty, and experiments using the FATES model to explore PFT competitive dynamics and the dynamics of size and age distributions in responses to changing climate and CO2.

A Matter of Timing: Identifying Significant Multi-Dose Radiotherapy Improvements by Numerical Simulation and Genetic Algorithm Search

PubMed Central

Angus, Simon D.; Piotrowska, Monika Joanna

2014-01-01

Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17–18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost-effecitive means of significantly improving clinical efficacy. PMID:25460164

A matter of timing: identifying significant multi-dose radiotherapy improvements by numerical simulation and genetic algorithm search.

PubMed

Angus, Simon D; Piotrowska, Monika Joanna

2014-01-01

Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17-18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost-effecitive means of significantly improving clinical efficacy.

Short-Term Forecasts Using NU-WRF for the Winter Olympics 2018

NASA Technical Reports Server (NTRS)

Srikishen, Jayanthi; Case, Jonathan L.; Petersen, Walter A.; Iguchi, Takamichi; Tao, Wei-Kuo; Zavodsky, Bradley T.; Molthan, Andrew

2017-01-01

The NASA Unified-Weather Research and Forecasting model (NU-WRF) will be included for testing and evaluation in the forecast demonstration project (FDP) of the International Collaborative Experiment -PyeongChang 2018 Olympic and Paralympic (ICE-POP) Winter Games. An international array of radar and supporting ground based observations together with various forecast and now-cast models will be operational during ICE-POP. In conjunction with personnel from NASA's Goddard Space Flight Center, the NASA Short-term Prediction Research and Transition (SPoRT) Center is developing benchmark simulations for a real-time NU-WRF configuration to run during the FDP. ICE-POP observational datasets will be used to validate model simulations and investigate improved model physics and performance for prediction of snow events during the research phase (RDP) of the project The NU-WRF model simulations will also support NASA Global Precipitation Measurement (GPM) Mission ground-validation physical and direct validation activities in relation to verifying, testing and improving satellite-based snowfall retrieval algorithms over complex terrain.

CFD simulation of reverse water-hammer induced by collapse of draft-tube cavity in a model pump-turbine during runaway process

NASA Astrophysics Data System (ADS)

Zhang, Xiaoxi; Cheng, Yongguang; Xia, Linsheng; Yang, Jiandong

2016-11-01

This paper reports the preliminary progress in the CFD simulation of the reverse water-hammer induced by the collapse of a draft-tube cavity in a model pump-turbine during the runaway process. Firstly, the Fluent customized 1D-3D coupling model for hydraulic transients and the Schnerr & Sauer cavitation model for cavity development are introduced. Then, the methods are validated by simulating the benchmark reverse water-hammer in a long pipe caused by a valve instant closure. The simulated head history at the valve agrees well with the measured data in literature. After that, the more complicated reverse water-hammer in the draft-tube of a runaway model pump-turbine, which is installed in a model pumped-storage power plant, is simulated. The dynamic processes of a vapor cavity, from generation, expansion, shrink to collapse, are shown. After the cavity collapsed, a sudden increase of pressure can be evidently observed. The process is featured by a locally expending and collapsing vapor cavity that is around the runner cone, which is different from the conventional recognition of violent water- column separation. This work reveals the possibility for simulating the reverse water-hammer phenomenon in turbines by 3D CFD.

IgSimulator: a versatile immunosequencing simulator.

PubMed

Safonova, Yana; Lapidus, Alla; Lill, Jennie

2015-10-01

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available. Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation. IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator. safonova.yana@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Benchmarks for target tracking

NASA Astrophysics Data System (ADS)

Dunham, Darin T.; West, Philip D.

2011-09-01

The term benchmark originates from the chiseled horizontal marks that surveyors made, into which an angle-iron could be placed to bracket ("bench") a leveling rod, thus ensuring that the leveling rod can be repositioned in exactly the same place in the future. A benchmark in computer terms is the result of running a computer program, or a set of programs, in order to assess the relative performance of an object by running a number of standard tests and trials against it. This paper will discuss the history of simulation benchmarks that are being used by multiple branches of the military and agencies of the US government. These benchmarks range from missile defense applications to chemical biological situations. Typically, a benchmark is used with Monte Carlo runs in order to tease out how algorithms deal with variability and the range of possible inputs. We will also describe problems that can be solved by a benchmark.

Modeling Electrokinetic Flows by the Smoothed Profile Method

PubMed Central

Luo, Xian; Beskok, Ali; Karniadakis, George Em

2010-01-01

We propose an efficient modeling method for electrokinetic flows based on the Smoothed Profile Method (SPM) [1–4] and spectral element discretizations. The new method allows for arbitrary differences in the electrical conductivities between the charged surfaces and the the surrounding electrolyte solution. The electrokinetic forces are included into the flow equations so that the Poisson-Boltzmann and electric charge continuity equations are cast into forms suitable for SPM. The method is validated by benchmark problems of electroosmotic flow in straight channels and electrophoresis of charged cylinders. We also present simulation results of electrophoresis of charged microtubules, and show that the simulated electrophoretic mobility and anisotropy agree with the experimental values. PMID:20352076

Benchmarking of Computational Models for NDE and SHM of Composites

NASA Technical Reports Server (NTRS)

Wheeler, Kevin; Leckey, Cara; Hafiychuk, Vasyl; Juarez, Peter; Timucin, Dogan; Schuet, Stefan; Hafiychuk, Halyna

2016-01-01

Ultrasonic wave phenomena constitute the leading physical mechanism for nondestructive evaluation (NDE) and structural health monitoring (SHM) of solid composite materials such as carbon-fiber-reinforced polymer (CFRP) laminates. Computational models of ultrasonic guided-wave excitation, propagation, scattering, and detection in quasi-isotropic laminates can be extremely valuable in designing practically realizable NDE and SHM hardware and software with desired accuracy, reliability, efficiency, and coverage. This paper presents comparisons of guided-wave simulations for CFRP composites implemented using three different simulation codes: two commercial finite-element analysis packages, COMSOL and ABAQUS, and a custom code implementing the Elastodynamic Finite Integration Technique (EFIT). Comparisons are also made to experimental laser Doppler vibrometry data and theoretical dispersion curves.

Large-eddy simulation of a backward facing step flow using a least-squares spectral element method

NASA Technical Reports Server (NTRS)

Chan, Daniel C.; Mittal, Rajat

1996-01-01

We report preliminary results obtained from the large eddy simulation of a backward facing step at a Reynolds number of 5100. The numerical platform is based on a high order Legendre spectral element spatial discretization and a least squares time integration scheme. A non-reflective outflow boundary condition is in place to minimize the effect of downstream influence. Smagorinsky model with Van Driest near wall damping is used for sub-grid scale modeling. Comparisons of mean velocity profiles and wall pressure show good agreement with benchmark data. More studies are needed to evaluate the sensitivity of this method on numerical parameters before it is applied to complex engineering problems.

A hybridizable discontinuous Galerkin method for modeling fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sheldon, Jason P.; Miller, Scott T.; Pitt, Jonathan S.

2016-12-01

This work presents a novel application of the hybridizable discontinuous Galerkin (HDG) finite element method to the multi-physics simulation of coupled fluid-structure interaction (FSI) problems. Recent applications of the HDG method have primarily been for single-physics problems including both solids and fluids, which are necessary building blocks for FSI modeling. Utilizing these established models, HDG formulations for linear elastostatics, a nonlinear elastodynamic model, and arbitrary Lagrangian-Eulerian Navier-Stokes are derived. The elasticity formulations are written in a Lagrangian reference frame, with the nonlinear formulation restricted to hyperelastic materials. With these individual solid and fluid formulations, the remaining challenge in FSI modeling is coupling together their disparate mathematics on the fluid-solid interface. This coupling is presented, along with the resultant HDG FSI formulation. Verification of the component models, through the method of manufactured solutions, is performed and each model is shown to converge at the expected rate. The individual components, along with the complete FSI model, are then compared to the benchmark problems proposed by Turek and Hron [1]. The solutions from the HDG formulation presented in this work trend towards the benchmark as the spatial polynomial order and the temporal order of integration are increased.

Probabilistic parameter estimation in a 2-step chemical kinetics model for n-dodecane jet autoignition

NASA Astrophysics Data System (ADS)

Hakim, Layal; Lacaze, Guilhem; Khalil, Mohammad; Sargsyan, Khachik; Najm, Habib; Oefelein, Joseph

2018-05-01

This paper demonstrates the development of a simple chemical kinetics model designed for autoignition of n-dodecane in air using Bayesian inference with a model-error representation. The model error, i.e. intrinsic discrepancy from a high-fidelity benchmark model, is represented by allowing additional variability in selected parameters. Subsequently, we quantify predictive uncertainties in the results of autoignition simulations of homogeneous reactors at realistic diesel engine conditions. We demonstrate that these predictive error bars capture model error as well. The uncertainty propagation is performed using non-intrusive spectral projection that can also be used in principle with larger scale computations, such as large eddy simulation. While the present calibration is performed to match a skeletal mechanism, it can be done with equal success using experimental data only (e.g. shock-tube measurements). Since our method captures the error associated with structural model simplifications, we believe that the optimised model could then lead to better qualified predictions of autoignition delay time in high-fidelity large eddy simulations than the existing detailed mechanisms. This methodology provides a way to reduce the cost of reaction kinetics in simulations systematically, while quantifying the accuracy of predictions of important target quantities.

Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations.

PubMed

Reumann, Matthias; Fitch, Blake G; Rayshubskiy, Aleksandr; Pitman, Michael C; Rice, John J

2011-06-01

We present the orthogonal recursive bisection algorithm that hierarchically segments the anatomical model structure into subvolumes that are distributed to cores. The anatomy is derived from the Visible Human Project, with electrophysiology based on the FitzHugh-Nagumo (FHN) and ten Tusscher (TT04) models with monodomain diffusion. Benchmark simulations with up to 16,384 and 32,768 cores on IBM Blue Gene/P and L supercomputers for both FHN and TT04 results show good load balancing with almost perfect speedup factors that are close to linear with the number of cores. Hence, strong scaling is demonstrated. With 32,768 cores, a 1000 ms simulation of full heart beat requires about 6.5 min of wall clock time for a simulation of the FHN model. For the largest machine partitions, the simulations execute at a rate of 0.548 s (BG/P) and 0.394 s (BG/L) of wall clock time per 1 ms of simulation time. To our knowledge, these simulations show strong scaling to substantially higher numbers of cores than reported previously for organ-level simulation of the heart, thus significantly reducing run times. The ability to reduce runtimes could play a critical role in enabling wider use of cardiac models in research and clinical applications.

Connected word recognition using a cascaded neuro-computational model

NASA Astrophysics Data System (ADS)

Hoya, Tetsuya; van Leeuwen, Cees

2016-10-01

We propose a novel framework for processing a continuous speech stream that contains a varying number of words, as well as non-speech periods. Speech samples are segmented into word-tokens and non-speech periods. An augmented version of an earlier-proposed, cascaded neuro-computational model is used for recognising individual words within the stream. Simulation studies using both a multi-speaker-dependent and speaker-independent digit string database show that the proposed method yields a recognition performance comparable to that obtained by a benchmark approach using hidden Markov models with embedded training.

Polymorphous Computing Architecture (PCA) Kernel Benchmark Measurements on the MIT Raw Microprocessor

DTIC Science & Technology

2006-06-14

Robert Graybill . A Raw hoard for the use of this project was provided by the Computer Architecture Croup at the Massachusetts Institute of Technology...simulator is presented by MIT as being an accurate model of the Raw chip, we have found that it does not accurately model the board. Our comparison...G4 processor, model 7410. with a 32 kbyte level-1 cache on-chip and a 2 Mbyte L2 cache connected through a 250 MH/ bus [12]. Each node has 256 Mbyte

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode calculations. First, we developed a gyrokinetic code capable of simulating long wavelengths using a fluid electron model [Chen 2015]. We benchmarked this code with an eigenmode calculation. Besides having to rewrite the field solver due to the breakdown in the gyrokinetic ordering for long wavelengths, very high radial resolution was required. We developed a technique where we used the solution from the eigenmode solver to specify radial boundary conditions allowing for a very high radial resolution of the inner solution. Using this technique enabled us to use our direct algorithm with gyrokinetic ions and drift kinetic electrons [Chen 2016]. This work was highlighted in an Invited Talk at the American Physical Society - Division of Plasma Physics in 2015.« less

MCNP HPGe detector benchmark with previously validated Cyltran model.

PubMed

Hau, I D; Russ, W R; Bronson, F

2009-05-01

An exact copy of the detector model generated for Cyltran was reproduced as an MCNP input file and the detection efficiency was calculated similarly with the methodology used in previous experimental measurements and simulation of a 280 cm(3) HPGe detector. Below 1000 keV the MCNP data correlated to the Cyltran results within 0.5% while above this energy the difference between MCNP and Cyltran increased to about 6% at 4800 keV, depending on the electron cut-off energy.

On the development of a comprehensive MC simulation model for the Gamma Knife Perfexion radiosurgery unit

NASA Astrophysics Data System (ADS)

Pappas, E. P.; Moutsatsos, A.; Pantelis, E.; Zoros, E.; Georgiou, E.; Torrens, M.; Karaiskos, P.

2016-02-01

This work presents a comprehensive Monte Carlo (MC) simulation model for the Gamma Knife Perfexion (PFX) radiosurgery unit. Model-based dosimetry calculations were benchmarked in terms of relative dose profiles (RDPs) and output factors (OFs), against corresponding EBT2 measurements. To reduce the rather prolonged computational time associated with the comprehensive PFX model MC simulations, two approximations were explored and evaluated on the grounds of dosimetric accuracy. The first consists in directional biasing of the 60Co photon emission while the second refers to the implementation of simplified source geometric models. The effect of the dose scoring volume dimensions in OF calculations accuracy was also explored. RDP calculations for the comprehensive PFX model were found to be in agreement with corresponding EBT2 measurements. Output factors of 0.819  ±  0.004 and 0.8941  ±  0.0013 were calculated for the 4 mm and 8 mm collimator, respectively, which agree, within uncertainties, with corresponding EBT2 measurements and published experimental data. Volume averaging was found to affect OF results by more than 0.3% for scoring volume radii greater than 0.5 mm and 1.4 mm for the 4 mm and 8 mm collimators, respectively. Directional biasing of photon emission resulted in a time efficiency gain factor of up to 210 with respect to the isotropic photon emission. Although no considerable effect on relative dose profiles was detected, directional biasing led to OF overestimations which were more pronounced for the 4 mm collimator and increased with decreasing emission cone half-angle, reaching up to 6% for a 5° angle. Implementation of simplified source models revealed that omitting the sources’ stainless steel capsule significantly affects both OF results and relative dose profiles, while the aluminum-based bushing did not exhibit considerable dosimetric effect. In conclusion, the results of this work suggest that any PFX simulation model should be benchmarked in terms of both RDP and OF results.

Qualification of CASMO5 / SIMULATE-3K against the SPERT-III E-core cold start-up experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grandi, G.; Moberg, L.

SIMULATE-3K is a three-dimensional kinetic code applicable to LWR Reactivity Initiated Accidents. S3K has been used to calculate several international recognized benchmarks. However, the feedback models in the benchmark exercises are different from the feedback models that SIMULATE-3K uses for LWR reactors. For this reason, it is worth comparing the SIMULATE-3K capabilities for Reactivity Initiated Accidents against kinetic experiments. The Special Power Excursion Reactor Test III was a pressurized-water, nuclear-research facility constructed to analyze the reactor kinetic behavior under initial conditions similar to those of commercial LWRs. The SPERT III E-core resembles a PWR in terms of fuel type, moderator,more » coolant flow rate, and system pressure. The initial test conditions (power, core flow, system pressure, core inlet temperature) are representative of cold start-up, hot start-up, hot standby, and hot full power. The qualification of S3K against the SPERT III E-core measurements is an ongoing work at Studsvik. In this paper, the results for the 30 cold start-up tests are presented. The results show good agreement with the experiments for the reactivity initiated accident main parameters: peak power, energy release and compensated reactivity. Predicted and measured peak powers differ at most by 13%. Measured and predicted reactivity compensations at the time of the peak power differ less than 0.01 $. Predicted and measured energy release differ at most by 13%. All differences are within the experimental uncertainty. (authors)« less

Experimental validation of the TOPAS Monte Carlo system for passive scattering proton therapy

PubMed Central

Testa, M.; Schümann, J.; Lu, H.-M.; Shin, J.; Faddegon, B.; Perl, J.; Paganetti, H.

2013-01-01

Purpose: TOPAS (TOol for PArticle Simulation) is a particle simulation code recently developed with the specific aim of making Monte Carlo simulations user-friendly for research and clinical physicists in the particle therapy community. The authors present a thorough and extensive experimental validation of Monte Carlo simulations performed with TOPAS in a variety of setups relevant for proton therapy applications. The set of validation measurements performed in this work represents an overall end-to-end testing strategy recommended for all clinical centers planning to rely on TOPAS for quality assurance or patient dose calculation and, more generally, for all the institutions using passive-scattering proton therapy systems. Methods: The authors systematically compared TOPAS simulations with measurements that are performed routinely within the quality assurance (QA) program in our institution as well as experiments specifically designed for this validation study. First, the authors compared TOPAS simulations with measurements of depth-dose curves for spread-out Bragg peak (SOBP) fields. Second, absolute dosimetry simulations were benchmarked against measured machine output factors (OFs). Third, the authors simulated and measured 2D dose profiles and analyzed the differences in terms of field flatness and symmetry and usable field size. Fourth, the authors designed a simple experiment using a half-beam shifter to assess the effects of multiple Coulomb scattering, beam divergence, and inverse square attenuation on lateral and longitudinal dose profiles measured and simulated in a water phantom. Fifth, TOPAS’ capabilities to simulate time dependent beam delivery was benchmarked against dose rate functions (i.e., dose per unit time vs time) measured at different depths inside an SOBP field. Sixth, simulations of the charge deposited by protons fully stopping in two different types of multilayer Faraday cups (MLFCs) were compared with measurements to benchmark the nuclear interaction models used in the simulations. Results: SOBPs’ range and modulation width were reproduced, on average, with an accuracy of +1, −2 and ±3 mm, respectively. OF simulations reproduced measured data within ±3%. Simulated 2D dose-profiles show field flatness and average field radius within ±3% of measured profiles. The field symmetry resulted, on average in ±3% agreement with commissioned profiles. TOPAS accuracy in reproducing measured dose profiles downstream the half beam shifter is better than 2%. Dose rate function simulation reproduced the measurements within ∼2% showing that the four-dimensional modeling of the passively modulation system was implement correctly and millimeter accuracy can be achieved in reproducing measured data. For MLFCs simulations, 2% agreement was found between TOPAS and both sets of experimental measurements. The overall results show that TOPAS simulations are within the clinical accepted tolerances for all QA measurements performed at our institution. Conclusions: Our Monte Carlo simulations reproduced accurately the experimental data acquired through all the measurements performed in this study. Thus, TOPAS can reliably be applied to quality assurance for proton therapy and also as an input for commissioning of commercial treatment planning systems. This work also provides the basis for routine clinical dose calculations in patients for all passive scattering proton therapy centers using TOPAS. PMID:24320505

Benchmarking Heavy Ion Transport Codes FLUKA, HETC-HEDS MARS15, MCNPX, and PHITS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronningen, Reginald Martin; Remec, Igor; Heilbronn, Lawrence H.

Powerful accelerators such as spallation neutron sources, muon-collider/neutrino facilities, and rare isotope beam facilities must be designed with the consideration that they handle the beam power reliably and safely, and they must be optimized to yield maximum performance relative to their design requirements. The simulation codes used for design purposes must produce reliable results. If not, component and facility designs can become costly, have limited lifetime and usefulness, and could even be unsafe. The objective of this proposal is to assess the performance of the currently available codes PHITS, FLUKA, MARS15, MCNPX, and HETC-HEDS that could be used for designmore » simulations involving heavy ion transport. We plan to access their performance by performing simulations and comparing results against experimental data of benchmark quality. Quantitative knowledge of the biases and the uncertainties of the simulations is essential as this potentially impacts the safe, reliable and cost effective design of any future radioactive ion beam facility. Further benchmarking of heavy-ion transport codes was one of the actions recommended in the Report of the 2003 RIA R&D Workshop".« less

Benchmarking MARS (accident management software) with the Browns Ferry fire

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawson, S.M.; Liu, L.Y.; Raines, J.C.

1992-01-01

The MAAP Accident Response System (MARS) is a userfriendly computer software developed to provide management and engineering staff with the most needed insights, during actual or simulated accidents, of the current and future conditions of the plant based on current plant data and its trends. To demonstrate the reliability of the MARS code in simulatng a plant transient, MARS is being benchmarked with the available reactor pressure vessel (RPV) pressure and level data from the Browns Ferry fire. The MRS software uses the Modular Accident Analysis Program (MAAP) code as its basis to calculate plant response under accident conditions. MARSmore » uses a limited set of plant data to initialize and track the accidnt progression. To perform this benchmark, a simulated set of plant data was constructed based on actual report data containing the information necessary to initialize MARS and keep track of plant system status throughout the accident progression. The initial Browns Ferry fire data were produced by performing a MAAP run to simulate the accident. The remaining accident simulation used actual plant data.« less

Excore Modeling with VERAShift

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandya, Tara M.; Evans, Thomas M.

It is important to be able to accurately predict the neutron flux outside the immediate reactor core for a variety of safety and material analyses. Monte Carlo radiation transport calculations are required to produce the high fidelity excore responses. Under this milestone VERA (specifically the VERAShift package) has been extended to perform excore calculations by running radiation transport calculations with Shift. This package couples VERA-CS with Shift to perform excore tallies for multiple state points concurrently, with each component capable of parallel execution on independent domains. Specifically, this package performs fluence calculations in the core barrel and vessel, or, performsmore » the requested tallies in any user-defined excore regions. VERAShift takes advantage of the general geometry package in Shift. This gives VERAShift the flexibility to explicitly model features outside the core barrel, including detailed vessel models, detectors, and power plant details. A very limited set of experimental and numerical benchmarks is available for excore simulation comparison. The Consortium for the Advanced Simulation of Light Water Reactors (CASL) has developed a set of excore benchmark problems to include as part of the VERA-CS verification and validation (V&V) problems. The excore capability in VERAShift has been tested on small representative assembly problems, multiassembly problems, and quarter-core problems. VERAView has also been extended to visualize these vessel fluence results from VERAShift. Preliminary vessel fluence results for quarter-core multistate calculations look very promising. Further development is needed to determine the details relevant to excore simulations. Validation of VERA for fluence and excore detectors still needs to be performed against experimental and numerical results.« less

Numerical modeling of separated flows at moderate Reynolds numbers appropriate for turbine blades and unmanned aero vehicles

NASA Astrophysics Data System (ADS)

Castiglioni, Giacomo

Flows over airfoils and blades in rotating machinery, for unmanned and micro-aerial vehicles, wind turbines, and propellers consist of a laminar boundary layer near the leading edge that is often followed by a laminar separation bubble and transition to turbulence further downstream. Typical Reynolds averaged Navier-Stokes turbulence models are inadequate for such flows. Direct numerical simulation is the most reliable, but is also the most computationally expensive alternative. This work assesses the capability of immersed boundary methods and large eddy simulations to reduce the computational requirements for such flows and still provide high quality results. Two-dimensional and three-dimensional simulations of a laminar separation bubble on a NACA-0012 airfoil at Rec = 5x104 and at 5° of incidence have been performed with an immersed boundary code and a commercial code using body fitted grids. Several sub-grid scale models have been implemented in both codes and their performance evaluated. For the two-dimensional simulations with the immersed boundary method the results show good agreement with the direct numerical simulation benchmark data for the pressure coefficient Cp and the friction coefficient Cf, but only when using dissipative numerical schemes. There is evidence that this behavior can be attributed to the ability of dissipative schemes to damp numerical noise coming from the immersed boundary. For the three-dimensional simulations the results show a good prediction of the separation point, but an inaccurate prediction of the reattachment point unless full direct numerical simulation resolution is used. The commercial code shows good agreement with the direct numerical simulation benchmark data in both two and three-dimensional simulations, but the presence of significant, unquantified numerical dissipation prevents a conclusive assessment of the actual prediction capabilities of very coarse large eddy simulations with low order schemes in general cases. Additionally, a two-dimensional sweep of angles of attack from 0° to 5° is performed showing a qualitative prediction of the jump in lift and drag coefficients due to the appearance of the laminar separation bubble. The numerical dissipation inhibits the predictive capabilities of large eddy simulations whenever it is of the same order of magnitude or larger than the sub-grid scale dissipation. The need to estimate the numerical dissipation is most pressing for low-order methods employed by commercial computational fluid dynamics codes. Following the recent work of Schranner et al., the equations and procedure for estimating the numerical dissipation rate and the numerical viscosity in a commercial code are presented. The method allows for the computation of the numerical dissipation rate and numerical viscosity in the physical space for arbitrary sub-domains in a self-consistent way, using only information provided by the code in question. The method is first tested for a three-dimensional Taylor-Green vortex flow in a simple cubic domain and compared with benchmark results obtained using an accurate, incompressible spectral solver. Afterwards the same procedure is applied for the first time to a realistic flow configuration, specifically to the above discussed laminar separation bubble flow over a NACA 0012 airfoil. The method appears to be quite robust and its application reveals that for the code and the flow in question the numerical dissipation can be significantly larger than the viscous dissipation or the dissipation of the classical Smagorinsky sub-grid scale model, confirming the previously qualitative finding.

The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison phase results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Rühaak, Wolfram

2016-04-01

Climate change impacts in permafrost regions have received considerable attention recently due to the pronounced warming trends experienced in recent decades and which have been projected into the future. Large portions of these permafrost regions are characterized by surface water bodies (lakes, rivers) that interact with the surrounding permafrost often generating taliks (unfrozen zones) within the permafrost that allow for hydrologic interactions between the surface water bodies and underlying aquifers and thus influence the hydrologic response of a landscape to climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model past and future evolution such units (Kurylyk et al. 2014). However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, which can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. A benchmark exercise was initialized at the end of 2014. Participants convened from USA, Canada, Europe, representing 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones (Kurylyk et al. 2014; Grenier et al. in prep.; Rühaak et al. 2015). They range from simpler, purely thermal 1D cases to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in a cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test case databases at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases TH2 & TH3. Both cases are essentially theoretical but include the full complexity of the coupled non-linear set of equations (heat transfer with conduction, advection, phase change and Darcian flow). The complete set of inter-comparison results shows that the participating codes all produce simulations which are quantitatively similar and correspond to physical intuition. From a quantitative perspective, they agree well over the whole set of performance measures. The differences among the simulation results will be discussed in more depth throughout the test cases especially for the identification of the threshold times for each system as these exhibited the least agreement. However, the results suggest that in spite of the difficulties associated with the resolution of the set of TH equations (coupled and non-linear structure with phase change providing steep slopes), the developed codes provide robust results with a qualitatively reasonable representation of the processes and offer a quantitatively realistic basis. Further perspectives of the exercise will also be presented.

A hybridizable discontinuous Galerkin method for modeling fluid–structure interaction

DOE PAGES

Sheldon, Jason P.; Miller, Scott T.; Pitt, Jonathan S.

2016-08-31

This study presents a novel application of the hybridizable discontinuous Galerkin (HDG) finite element method to the multi-physics simulation of coupled fluid–structure interaction (FSI) problems. Recent applications of the HDG method have primarily been for single-physics problems including both solids and fluids, which are necessary building blocks for FSI modeling. Utilizing these established models, HDG formulations for linear elastostatics, a nonlinear elastodynamic model, and arbitrary Lagrangian–Eulerian Navier–Stokes are derived. The elasticity formulations are written in a Lagrangian reference frame, with the nonlinear formulation restricted to hyperelastic materials. With these individual solid and fluid formulations, the remaining challenge in FSI modelingmore » is coupling together their disparate mathematics on the fluid–solid interface. This coupling is presented, along with the resultant HDG FSI formulation. Verification of the component models, through the method of manufactured solutions, is performed and each model is shown to converge at the expected rate. The individual components, along with the complete FSI model, are then compared to the benchmark problems proposed by Turek and Hron [1]. The solutions from the HDG formulation presented in this work trend towards the benchmark as the spatial polynomial order and the temporal order of integration are increased.« less

Benchmarking: applications to transfusion medicine.

PubMed

Apelseth, Torunn Oveland; Molnar, Laura; Arnold, Emmy; Heddle, Nancy M

2012-10-01

Benchmarking is as a structured continuous collaborative process in which comparisons for selected indicators are used to identify factors that, when implemented, will improve transfusion practices. This study aimed to identify transfusion medicine studies reporting on benchmarking, summarize the benchmarking approaches used, and identify important considerations to move the concept of benchmarking forward in the field of transfusion medicine. A systematic review of published literature was performed to identify transfusion medicine-related studies that compared at least 2 separate institutions or regions with the intention of benchmarking focusing on 4 areas: blood utilization, safety, operational aspects, and blood donation. Forty-five studies were included: blood utilization (n = 35), safety (n = 5), operational aspects of transfusion medicine (n = 5), and blood donation (n = 0). Based on predefined criteria, 7 publications were classified as benchmarking, 2 as trending, and 36 as single-event studies. Three models of benchmarking are described: (1) a regional benchmarking program that collects and links relevant data from existing electronic sources, (2) a sentinel site model where data from a limited number of sites are collected, and (3) an institutional-initiated model where a site identifies indicators of interest and approaches other institutions. Benchmarking approaches are needed in the field of transfusion medicine. Major challenges include defining best practices and developing cost-effective methods of data collection. For those interested in initiating a benchmarking program, the sentinel site model may be most effective and sustainable as a starting point, although the regional model would be the ideal goal. Copyright © 2012 Elsevier Inc. All rights reserved.

Opto-Electronic and Interconnects Hierarchical Design Automation System (OE-IDEAS)

DTIC Science & Technology

2004-05-01

NETBOOK WEBSITE............................................................71 8.2 SIMULATION OF CRITICAL PATH FROM THE MAYO “10G” SYSTEM MCM BOARD...Benchmarks from the DaVinci Netbook website In May 2002, CFDRC downloaded all the materials from the DaVinci Netbook website containing the benchmark

Benchmarking Using Basic DBMS Operations

NASA Astrophysics Data System (ADS)

Crolotte, Alain; Ghazal, Ahmad

The TPC-H benchmark proved to be successful in the decision support area. Many commercial database vendors and their related hardware vendors used these benchmarks to show the superiority and competitive edge of their products. However, over time, the TPC-H became less representative of industry trends as vendors keep tuning their database to this benchmark-specific workload. In this paper, we present XMarq, a simple benchmark framework that can be used to compare various software/hardware combinations. Our benchmark model is currently composed of 25 queries that measure the performance of basic operations such as scans, aggregations, joins and index access. This benchmark model is based on the TPC-H data model due to its maturity and well-understood data generation capability. We also propose metrics to evaluate single-system performance and compare two systems. Finally we illustrate the effectiveness of this model by showing experimental results comparing two systems under different conditions.

Simulation for analysis and control of superplastic forming. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zacharia, T.; Aramayo, G.A.; Simunovic, S.

1996-08-01

A joint study was conducted by Oak Ridge National Laboratory (ORNL) and the Pacific Northwest Laboratory (PNL) for the U.S. Department of Energy-Lightweight Materials (DOE-LWM) Program. the purpose of the study was to assess and benchmark the current modeling capabilities with respect to accuracy of predictions and simulation time. Two modeling capabilities with respect to accuracy of predictions and simulation time. Two simulation platforms were considered in this study, which included the LS-DYNA3D code installed on ORNL`s high- performance computers and the finite element code MARC used at PNL. both ORNL and PNL performed superplastic forming (SPF) analysis on amore » standard butter-tray geometry, which was defined by PNL, to better understand the capabilities of the respective models. The specific geometry was selected and formed at PNL, and the experimental results, such as forming time and thickness at specific locations, were provided for comparisons with numerical predictions. Furthermore, comparisons between the ORNL simulation results, using elasto-plastic analysis, and PNL`s results, using rigid-plastic flow analysis, were performed.« less

Interfacing the Generalized Fluid System Simulation Program with the SINDA/G Thermal Program

NASA Technical Reports Server (NTRS)

Schallhorn, Paul; Palmiter, Christopher; Farmer, Jeffery; Lycans, Randall; Tiller, Bruce

2000-01-01

A general purpose, one dimensional fluid flow code has been interfaced with the thermal analysis program SINDA/G. The flow code, GFSSP, is capable of analyzing steady state and transient flow in a complex network. The flow code is capable of modeling several physical phenomena including compressibility effects, phase changes, body forces (such as gravity and centrifugal) and mixture thermodynamics for multiple species. The addition of GFSSP to SINDA/G provides a significant improvement in convective heat transfer modeling for SINDA/G. The interface development was conducted in two phases. This paper describes the first (which allows for steady and quasi-steady - unsteady solid, steady fluid - conjugate heat transfer modeling). The second (full transient conjugate heat transfer modeling) phase of the interface development will be addressed in a later paper. Phase 1 development has been benchmarked to an analytical solution with excellent agreement. Additional test cases for each development phase demonstrate desired features of the interface. The results of the benchmark case, three additional test cases and a practical application are presented herein.

Center for Extended Magnetohydrodynamic Modeling Cooperative Agreement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carl R. Sovinec

The Center for Extended Magnetohydrodynamic Modeling (CEMM) is developing computer simulation models for predicting the behavior of magnetically confined plasmas. Over the first phase of support from the Department of Energy’s Scientific Discovery through Advanced Computing (SciDAC) initiative, the focus has been on macroscopic dynamics that alter the confinement properties of magnetic field configurations. The ultimate objective is to provide computational capabilities to predict plasma behavior—not unlike computational weather prediction—to optimize performance and to increase the reliability of magnetic confinement for fusion energy. Numerical modeling aids theoretical research by solving complicated mathematical models of plasma behavior including strong nonlinear effectsmore » and the influences of geometrical shaping of actual experiments. The numerical modeling itself remains an area of active research, due to challenges associated with simulating multiple temporal and spatial scales. The research summarized in this report spans computational and physical topics associated with state of the art simulation of magnetized plasmas. The tasks performed for this grant are categorized according to whether they are primarily computational, algorithmic, or application-oriented in nature. All involve the development and use of the Non-Ideal Magnetohydrodynamics with Rotation, Open Discussion (NIMROD) code, which is described at http://nimrodteam.org. With respect to computation, we have tested and refined methods for solving the large algebraic systems of equations that result from our numerical approximations of the physical model. Collaboration with the Terascale Optimal PDE Solvers (TOPS) SciDAC center led us to the SuperLU_DIST software library [http://crd.lbl.gov/~xiaoye/SuperLU/] for solving large sparse matrices using direct methods on parallel computers. Switching to this solver library boosted NIMROD’s performance by a factor of five in typical large nonlinear simulations, which has been publicized as a success story of SciDAC-fostered collaboration. Furthermore, the SuperLU software does not assume any mathematical symmetry, and its generality provides an important capability for extending the physical model beyond magnetohydrodynamics (MHD). With respect to algorithmic and model development, our most significant accomplishment is the development of a new method for solving plasma models that treat electrons as an independent plasma component. These ‘two-fluid’ models encompass MHD and add temporal and spatial scales that are beyond the response of the ion species. Implementation and testing of a previously published algorithm did not prove successful for NIMROD, and the new algorithm has since been devised, analyzed, and implemented. Two-fluid modeling, an important objective of the original NIMROD project, is now routine in 2D applications. Algorithmic components for 3D modeling are in place and tested; though, further computational work is still needed for efficiency. Other algorithmic work extends the ion-fluid stress tensor to include models for parallel and gyroviscous stresses. In addition, our hot-particle simulation capability received important refinements that permitted completion of a benchmark with the M3D code. A highlight of our applications work is the edge-localized mode (ELM) modeling, which was part of the first-ever computational Performance Target for the DOE Office of Fusion Energy Science, see http://www.science.doe.gov/ofes/performancetargets.shtml. Our efforts allowed MHD simulations to progress late into the nonlinear stage, where energy is conducted to the wall location. They also produced a two-fluid ELM simulation starting from experimental information and demonstrating critical drift effects that are characteristic of two-fluid physics. Another important application is the internal kink mode in a tokamak. Here, the primary purpose of the study has been to benchmark the two main code development lines of CEMM, NIMROD and M3D, on a relevant nonlinear problem. Results from the two codes show repeating nonlinear relaxation events driven by the kink mode over quantitatively comparable timescales. The work has launched a more comprehensive nonlinear benchmarking exercise, where realistic transport effects have an important role.« less

A Distributed Platform for Global-Scale Agent-Based Models of Disease Transmission

PubMed Central

Parker, Jon; Epstein, Joshua M.

2013-01-01

The Global-Scale Agent Model (GSAM) is presented. The GSAM is a high-performance distributed platform for agent-based epidemic modeling capable of simulating a disease outbreak in a population of several billion agents. It is unprecedented in its scale, its speed, and its use of Java. Solutions to multiple challenges inherent in distributing massive agent-based models are presented. Communication, synchronization, and memory usage are among the topics covered in detail. The memory usage discussion is Java specific. However, the communication and synchronization discussions apply broadly. We provide benchmarks illustrating the GSAM’s speed and scalability. PMID:24465120

Comparison of Homogeneous and Heterogeneous CFD Fuel Models for Phase I of the IAEA CRP on HTR Uncertainties Benchmark

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerhard Strydom; Su-Jong Yoon

2014-04-01

Computational Fluid Dynamics (CFD) evaluation of homogeneous and heterogeneous fuel models was performed as part of the Phase I calculations of the International Atomic Energy Agency (IAEA) Coordinate Research Program (CRP) on High Temperature Reactor (HTR) Uncertainties in Modeling (UAM). This study was focused on the nominal localized stand-alone fuel thermal response, as defined in Ex. I-3 and I-4 of the HTR UAM. The aim of the stand-alone thermal unit-cell simulation is to isolate the effect of material and boundary input uncertainties on a very simplified problem, before propagation of these uncertainties are performed in subsequent coupled neutronics/thermal fluids phasesmore » on the benchmark. In many of the previous studies for high temperature gas cooled reactors, the volume-averaged homogeneous mixture model of a single fuel compact has been applied. In the homogeneous model, the Tristructural Isotropic (TRISO) fuel particles in the fuel compact were not modeled directly and an effective thermal conductivity was employed for the thermo-physical properties of the fuel compact. On the contrary, in the heterogeneous model, the uranium carbide (UCO), inner and outer pyrolytic carbon (IPyC/OPyC) and silicon carbide (SiC) layers of the TRISO fuel particles are explicitly modeled. The fuel compact is modeled as a heterogeneous mixture of TRISO fuel kernels embedded in H-451 matrix graphite. In this study, a steady-state and transient CFD simulations were performed with both homogeneous and heterogeneous models to compare the thermal characteristics. The nominal values of the input parameters are used for this CFD analysis. In a future study, the effects of input uncertainties in the material properties and boundary parameters will be investigated and reported.« less

A regularized vortex-particle mesh method for large eddy simulation

NASA Astrophysics Data System (ADS)

Spietz, H. J.; Walther, J. H.; Hejlesen, M. M.

2017-11-01

We present recent developments of the remeshed vortex particle-mesh method for simulating incompressible fluid flow. The presented method relies on a parallel higher-order FFT based solver for the Poisson equation. Arbitrary high order is achieved through regularization of singular Green's function solutions to the Poisson equation and recently we have derived novel high order solutions for a mixture of open and periodic domains. With this approach the simulated variables may formally be viewed as the approximate solution to the filtered Navier Stokes equations, hence we use the method for Large Eddy Simulation by including a dynamic subfilter-scale model based on test-filters compatible with the aforementioned regularization functions. Further the subfilter-scale model uses Lagrangian averaging, which is a natural candidate in light of the Lagrangian nature of vortex particle methods. A multiresolution variation of the method is applied to simulate the benchmark problem of the flow past a square cylinder at Re = 22000 and the obtained results are compared to results from the literature.

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

Multidimensional Multiphysics Simulation of TRISO Particle Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. D. Hales; R. L. Williamson; S. R. Novascone

2013-11-01

Multidimensional multiphysics analysis of TRISO-coated particle fuel using the BISON finite-element based nuclear fuels code is described. The governing equations and material models applicable to particle fuel and implemented in BISON are outlined. Code verification based on a recent IAEA benchmarking exercise is described, and excellant comparisons are reported. Multiple TRISO-coated particles of increasing geometric complexity are considered. It is shown that the code's ability to perform large-scale parallel computations permits application to complex 3D phenomena while very efficient solutions for either 1D spherically symmetric or 2D axisymmetric geometries are straightforward. Additionally, the flexibility to easily include new physical andmore » material models and uncomplicated ability to couple to lower length scale simulations makes BISON a powerful tool for simulation of coated-particle fuel. Future code development activities and potential applications are identified.« less

Coupled Neutronics Thermal-Hydraulic Solution of a Full-Core PWR Using VERA-CS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clarno, Kevin T; Palmtag, Scott; Davidson, Gregory G

2014-01-01

The Consortium for Advanced Simulation of Light Water Reactors (CASL) is developing a core simulator called VERA-CS to model operating PWR reactors with high resolution. This paper describes how the development of VERA-CS is being driven by a set of progression benchmark problems that specify the delivery of useful capability in discrete steps. As part of this development, this paper will describe the current capability of VERA-CS to perform a multiphysics simulation of an operating PWR at Hot Full Power (HFP) conditions using a set of existing computer codes coupled together in a novel method. Results for several single-assembly casesmore » are shown that demonstrate coupling for different boron concentrations and power levels. Finally, high-resolution results are shown for a full-core PWR reactor modeled in quarter-symmetry.« less

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

Benchmarking gyrokinetic simulations in a toroidal flux-tube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Y.; Parker, S. E.; Wan, W.

2013-09-15

A flux-tube model is implemented in the global turbulence code GEM [Y. Chen and S. E. Parker, J. Comput. Phys. 220, 839 (2007)] in order to facilitate benchmarking with Eulerian codes. The global GEM assumes the magnetic equilibrium to be completely given. The initial flux-tube implementation simply selects a radial location as the center of the flux-tube and a radial size of the flux-tube, sets all equilibrium quantities (B, ∇B, etc.) to be equal to the values at the center of the flux-tube, and retains only a linear radial profile of the safety factor needed for boundary conditions. This implementationmore » shows disagreement with Eulerian codes in linear simulations. An alternative flux-tube model based on a complete local equilibrium solution of the Grad-Shafranov equation [J. Candy, Plasma Phys. Controlled Fusion 51, 105009 (2009)] is then implemented. This results in better agreement between Eulerian codes and the particle-in-cell (PIC) method. The PIC algorithm based on the v{sub ||}-formalism [J. Reynders, Ph.D. dissertation, Princeton University, 1992] and the gyrokinetic ion/fluid electron hybrid model with kinetic electron closure [Y. Chan and S. E. Parker, Phys. Plasmas 18, 055703 (2011)] are also implemented in the flux-tube geometry and compared with the direct method for both the ion temperature gradient driven modes and the kinetic ballooning modes.« less

Assessing the capability of continuum and discrete particle methods to simulate gas-solids flow using DNS predictions as a benchmark

DOE PAGES

Lu, Liqiang; Liu, Xiaowen; Li, Tingwen; ...

2017-08-12

For this study, gas–solids flow in a three-dimension periodic domain was numerically investigated by direct numerical simulation (DNS), computational fluid dynamic-discrete element method (CFD-DEM) and two-fluid model (TFM). DNS data obtained by finely resolving the flow around every particle are used as a benchmark to assess the validity of coarser DEM and TFM approaches. The CFD-DEM predicts the correct cluster size distribution and under-predicts the macro-scale slip velocity even with a grid size as small as twice the particle diameter. The TFM approach predicts larger cluster size and lower slip velocity with a homogeneous drag correlation. Although the slip velocitymore » can be matched by a simple modification to the drag model, the predicted voidage distribution is still different from DNS: Both CFD-DEM and TFM over-predict the fraction of particles in dense regions and under-predict the fraction of particles in regions of intermediate void fractions. Also, the cluster aspect ratio of DNS is smaller than CFD-DEM and TFM. Since a simple correction to the drag model can predict a correct slip velocity, it is hopeful that drag corrections based on more elaborate theories that consider voidage gradient and particle fluctuations may be able to improve the current predictions of cluster distribution.« less

Assessing the capability of continuum and discrete particle methods to simulate gas-solids flow using DNS predictions as a benchmark

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Liqiang; Liu, Xiaowen; Li, Tingwen

For this study, gas–solids flow in a three-dimension periodic domain was numerically investigated by direct numerical simulation (DNS), computational fluid dynamic-discrete element method (CFD-DEM) and two-fluid model (TFM). DNS data obtained by finely resolving the flow around every particle are used as a benchmark to assess the validity of coarser DEM and TFM approaches. The CFD-DEM predicts the correct cluster size distribution and under-predicts the macro-scale slip velocity even with a grid size as small as twice the particle diameter. The TFM approach predicts larger cluster size and lower slip velocity with a homogeneous drag correlation. Although the slip velocitymore » can be matched by a simple modification to the drag model, the predicted voidage distribution is still different from DNS: Both CFD-DEM and TFM over-predict the fraction of particles in dense regions and under-predict the fraction of particles in regions of intermediate void fractions. Also, the cluster aspect ratio of DNS is smaller than CFD-DEM and TFM. Since a simple correction to the drag model can predict a correct slip velocity, it is hopeful that drag corrections based on more elaborate theories that consider voidage gradient and particle fluctuations may be able to improve the current predictions of cluster distribution.« less

Real-time simulation of biological soft tissues: a PGD approach.

PubMed

Niroomandi, S; González, D; Alfaro, I; Bordeu, F; Leygue, A; Cueto, E; Chinesta, F

2013-05-01

We introduce here a novel approach for the numerical simulation of nonlinear, hyperelastic soft tissues at kilohertz feedback rates necessary for haptic rendering. This approach is based upon the use of proper generalized decomposition techniques, a generalization of PODs. Proper generalized decomposition techniques can be considered as a means of a priori model order reduction and provides a physics-based meta-model without the need for prior computer experiments. The suggested strategy is thus composed of an offline phase, in which a general meta-model is computed, and an online evaluation phase in which the results are obtained at real time. Results are provided that show the potential of the proposed technique, together with some benchmark test that shows the accuracy of the method. Copyright © 2013 John Wiley & Sons, Ltd.

Parallel 3D-TLM algorithm for simulation of the Earth-ionosphere cavity

NASA Astrophysics Data System (ADS)

Toledo-Redondo, Sergio; Salinas, Alfonso; Morente-Molinera, Juan Antonio; Méndez, Antonio; Fornieles, Jesús; Portí, Jorge; Morente, Juan Antonio

2013-03-01

A parallel 3D algorithm for solving time-domain electromagnetic problems with arbitrary geometries is presented. The technique employed is the Transmission Line Modeling (TLM) method implemented in Shared Memory (SM) environments. The benchmarking performed reveals that the maximum speedup depends on the memory size of the problem as well as multiple hardware factors, like the disposition of CPUs, cache, or memory. A maximum speedup of 15 has been measured for the largest problem. In certain circumstances of low memory requirements, superlinear speedup is achieved using our algorithm. The model is employed to model the Earth-ionosphere cavity, thus enabling a study of the natural electromagnetic phenomena that occur in it. The algorithm allows complete 3D simulations of the cavity with a resolution of 10 km, within a reasonable timescale.

76 T dwarfs from the UKIDSS LAS: benchmarks, kinematics and an updated space density

NASA Astrophysics Data System (ADS)

Burningham, Ben; Cardoso, C. V.; Smith, L.; Leggett, S. K.; Smart, R. L.; Mann, A. W.; Dhital, S.; Lucas, P. W.; Tinney, C. G.; Pinfield, D. J.; Zhang, Z.; Morley, C.; Saumon, D.; Aller, K.; Littlefair, S. P.; Homeier, D.; Lodieu, N.; Deacon, N.; Marley, M. S.; van Spaandonk, L.; Baker, D.; Allard, F.; Andrei, A. H.; Canty, J.; Clarke, J.; Day-Jones, A. C.; Dupuy, T.; Fortney, J. J.; Gomes, J.; Ishii, M.; Jones, H. R. A.; Liu, M.; Magazzú, A.; Marocco, F.; Murray, D. N.; Rojas-Ayala, B.; Tamura, M.

2013-07-01

We report the discovery of 76 new T dwarfs from the UKIRT Infrared Deep Sky Survey (UKIDSS) Large Area Survey (LAS). Near-infrared broad- and narrow-band photometry and spectroscopy are presented for the new objects, along with Wide-field Infrared Survey Explorer (WISE) and warm-Spitzer photometry. Proper motions for 128 UKIDSS T dwarfs are presented from a new two epoch LAS proper motion catalogue. We use these motions to identify two new benchmark systems: LHS 6176AB, a T8p+M4 pair and HD 118865AB, a T5.5+F8 pair. Using age constraints from the primaries and evolutionary models to constrain the radii, we have estimated their physical properties from their bolometric luminosity. We compare the colours and properties of known benchmark T dwarfs to the latest model atmospheres and draw two principal conclusions. First, it appears that the H - [4.5] and J - W2 colours are more sensitive to metallicity than has previously been recognized, such that differences in metallicity may dominate over differences in Teff when considering relative properties of cool objects using these colours. Secondly, the previously noted apparent dominance of young objects in the late-T dwarf sample is no longer apparent when using the new model grids and the expanded sample of late-T dwarfs and benchmarks. This is supported by the apparently similar distribution of late-T dwarfs and earlier type T dwarfs on reduced proper motion diagrams that we present. Finally, we present updated space densities for the late-T dwarfs, and compare our values to simulation predictions and those from WISE.

Backward-stochastic-differential-equation approach to modeling of gene expression

NASA Astrophysics Data System (ADS)

Shamarova, Evelina; Chertovskih, Roman; Ramos, Alexandre F.; Aguiar, Paulo

2017-03-01

In this article, we introduce a backward method to model stochastic gene expression and protein-level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation (BSDE). Unlike many other SDE techniques proposed in the literature, the BSDE method is backward in time; that is, instead of initial conditions it requires the specification of end-point ("final") conditions, in addition to the model parametrization. To validate our approach we employ Gillespie's stochastic simulation algorithm (SSA) to generate (forward) benchmark data, according to predefined gene network models. Numerical simulations show that the BSDE method is able to correctly infer the protein-level distributions that preceded a known final condition, obtained originally from the forward SSA. This makes the BSDE method a powerful systems biology tool for time-reversed simulations, allowing, for example, the assessment of the biological conditions (e.g., protein concentrations) that preceded an experimentally measured event of interest (e.g., mitosis, apoptosis, etc.).

Backward-stochastic-differential-equation approach to modeling of gene expression.

PubMed

Shamarova, Evelina; Chertovskih, Roman; Ramos, Alexandre F; Aguiar, Paulo

2017-03-01

In this article, we introduce a backward method to model stochastic gene expression and protein-level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation (BSDE). Unlike many other SDE techniques proposed in the literature, the BSDE method is backward in time; that is, instead of initial conditions it requires the specification of end-point ("final") conditions, in addition to the model parametrization. To validate our approach we employ Gillespie's stochastic simulation algorithm (SSA) to generate (forward) benchmark data, according to predefined gene network models. Numerical simulations show that the BSDE method is able to correctly infer the protein-level distributions that preceded a known final condition, obtained originally from the forward SSA. This makes the BSDE method a powerful systems biology tool for time-reversed simulations, allowing, for example, the assessment of the biological conditions (e.g., protein concentrations) that preceded an experimentally measured event of interest (e.g., mitosis, apoptosis, etc.).

Maxwell: A semi-analytic 4D code for earthquake cycle modeling of transform fault systems

NASA Astrophysics Data System (ADS)

Sandwell, David; Smith-Konter, Bridget

2018-05-01

We have developed a semi-analytic approach (and computational code) for rapidly calculating 3D time-dependent deformation and stress caused by screw dislocations imbedded within an elastic layer overlying a Maxwell viscoelastic half-space. The maxwell model is developed in the Fourier domain to exploit the computational advantages of the convolution theorem, hence substantially reducing the computational burden associated with an arbitrarily complex distribution of force couples necessary for fault modeling. The new aspect of this development is the ability to model lateral variations in shear modulus. Ten benchmark examples are provided for testing and verification of the algorithms and code. One final example simulates interseismic deformation along the San Andreas Fault System where lateral variations in shear modulus are included to simulate lateral variations in lithospheric structure.

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code.

PubMed

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling.

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code

PubMed Central

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling. PMID:28701946

A generic framework for individual-based modelling and physical-biological interaction

PubMed Central

2018-01-01

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems. PMID:29351280

Time Hierarchies and Model Reduction in Canonical Non-linear Models

PubMed Central

Löwe, Hannes; Kremling, Andreas; Marin-Sanguino, Alberto

2016-01-01

The time-scale hierarchies of a very general class of models in differential equations is analyzed. Classical methods for model reduction and time-scale analysis have been adapted to this formalism and a complementary method is proposed. A unified theoretical treatment shows how the structure of the system can be much better understood by inspection of two sets of singular values: one related to the stoichiometric structure of the system and another to its kinetics. The methods are exemplified first through a toy model, then a large synthetic network and finally with numeric simulations of three classical benchmark models of real biological systems. PMID:27708665

Simulations of the propagation of multiple-FM smoothing by spectral dispersion on OMEGA EP

DOE PAGES

Kelly, J. H.; Shvydky, A.; Marozas, J. A.; ...

2013-02-18

A one-dimensional (1-D) smoothing by spectral dispersion (SSD) system for smoothing focal-spot nonuniformities using multiple modulation frequencies has been commissioned on one long-pulse beamline of OMEGA EP, the first use of such a system in a high-energy laser. Frequency modulation (FM) to amplitude modulation (AM) conversion in the infrared (IR) output, frequency conversion, and final optics affected the accumulation of B-integral in that beamline. Modeling of this FM-to-AM conversion using the code Miró. was used as input to set the beamline performance limits for picket (short) pulses with multi-FM SSD applied. This article first describes that modeling. The 1-D SSDmore » analytical model of Chuang is first extended to the case of multiple modulators and then used to benchmark Miró simulations. Comparison is also made to an alternative analytic model developed by Hocquet et al. With the confidence engendered by this benchmarking, Miró results for multi-FM SSD applied on OMEGA EP are then presented. The relevant output section(s) of the OMEGA EP Laser System are described. The additional B-integral in OMEGA EP IR components upstream of the frequency converters due to AM is modeled. The importance of locating the image of the SSD dispersion grating at the frequency converters is demonstrated. In conclusion, since frequency conversion is not performed in OMEGA EP’s target chamber, the additional AM due to propagation to the target chamber’s vacuum window is modeled.« less

New insights into galaxy structure from GALPHAT- I. Motivation, methodology and benchmarks for Sérsic models

NASA Astrophysics Data System (ADS)

Yoon, Ilsang; Weinberg, Martin D.; Katz, Neal

2011-06-01

We introduce a new galaxy image decomposition tool, GALPHAT (GALaxy PHotometric ATtributes), which is a front-end application of the Bayesian Inference Engine (BIE), a parallel Markov chain Monte Carlo package, to provide full posterior probability distributions and reliable confidence intervals for all model parameters. The BIE relies on GALPHAT to compute the likelihood function. GALPHAT generates scale-free cumulative image tables for the desired model family with precise error control. Interpolation of this table yields accurate pixellated images with any centre, scale and inclination angle. GALPHAT then rotates the image by position angle using a Fourier shift theorem, yielding high-speed, accurate likelihood computation. We benchmark this approach using an ensemble of simulated Sérsic model galaxies over a wide range of observational conditions: the signal-to-noise ratio S/N, the ratio of galaxy size to the point spread function (PSF) and the image size, and errors in the assumed PSF; and a range of structural parameters: the half-light radius re and the Sérsic index n. We characterize the strength of parameter covariance in the Sérsic model, which increases with S/N and n, and the results strongly motivate the need for the full posterior probability distribution in galaxy morphology analyses and later inferences. The test results for simulated galaxies successfully demonstrate that, with a careful choice of Markov chain Monte Carlo algorithms and fast model image generation, GALPHAT is a powerful analysis tool for reliably inferring morphological parameters from a large ensemble of galaxies over a wide range of different observational conditions.

Comparisons between physics-based, engineering, and statistical learning models for outdoor sound propagation.

PubMed

Hart, Carl R; Reznicek, Nathan J; Wilson, D Keith; Pettit, Chris L; Nykaza, Edward T

2016-05-01

Many outdoor sound propagation models exist, ranging from highly complex physics-based simulations to simplified engineering calculations, and more recently, highly flexible statistical learning methods. Several engineering and statistical learning models are evaluated by using a particular physics-based model, namely, a Crank-Nicholson parabolic equation (CNPE), as a benchmark. Narrowband transmission loss values predicted with the CNPE, based upon a simulated data set of meteorological, boundary, and source conditions, act as simulated observations. In the simulated data set sound propagation conditions span from downward refracting to upward refracting, for acoustically hard and soft boundaries, and low frequencies. Engineering models used in the comparisons include the ISO 9613-2 method, Harmonoise, and Nord2000 propagation models. Statistical learning methods used in the comparisons include bagged decision tree regression, random forest regression, boosting regression, and artificial neural network models. Computed skill scores are relative to sound propagation in a homogeneous atmosphere over a rigid ground. Overall skill scores for the engineering noise models are 0.6%, -7.1%, and 83.8% for the ISO 9613-2, Harmonoise, and Nord2000 models, respectively. Overall skill scores for the statistical learning models are 99.5%, 99.5%, 99.6%, and 99.6% for bagged decision tree, random forest, boosting, and artificial neural network regression models, respectively.

Development of a two-fluid drag law for clustered particles using direct numerical simulation and validation through experiments

NASA Astrophysics Data System (ADS)

Abbasi Baharanchi, Ahmadreza

This dissertation focused on development and utilization of numerical and experimental approaches to improve the CFD modeling of fluidization flow of cohesive micron size particles. The specific objectives of this research were: (1) Developing a cluster prediction mechanism applicable to Two-Fluid Modeling (TFM) of gas-solid systems (2) Developing more accurate drag models for Two-Fluid Modeling (TFM) of gas-solid fluidization flow with the presence of cohesive interparticle forces (3) using the developed model to explore the improvement of accuracy of TFM in simulation of fluidization flow of cohesive powders (4) Understanding the causes and influential factor which led to improvements and quantification of improvements (5) Gathering data from a fast fluidization flow and use these data for benchmark validations. Simulation results with two developed cluster-aware drag models showed that cluster prediction could effectively influence the results in both the first and second cluster-aware models. It was proven that improvement of accuracy of TFM modeling using three versions of the first hybrid model was significant and the best improvements were obtained by using the smallest values of the switch parameter which led to capturing the smallest chances of cluster prediction. In the case of the second hybrid model, dependence of critical model parameter on only Reynolds number led to the fact that improvement of accuracy was significant only in dense section of the fluidized bed. This finding may suggest that a more sophisticated particle resolved DNS model, which can span wide range of solid volume fraction, can be used in the formulation of the cluster-aware drag model. The results of experiment suing high speed imaging indicated the presence of particle clusters in the fluidization flow of FCC inside the riser of FIU-CFB facility. In addition, pressure data was successfully captured along the fluidization column of the facility and used as benchmark validation data for the second hybrid model developed in the present dissertation. It was shown the second hybrid model could predict the pressure data in the dense section of the fluidization column with better accuracy.

A study of workstation computational performance for real-time flight simulation

NASA Technical Reports Server (NTRS)

Maddalon, Jeffrey M.; Cleveland, Jeff I., II

1995-01-01

With recent advances in microprocessor technology, some have suggested that modern workstations provide enough computational power to properly operate a real-time simulation. This paper presents the results of a computational benchmark, based on actual real-time flight simulation code used at Langley Research Center, which was executed on various workstation-class machines. The benchmark was executed on different machines from several companies including: CONVEX Computer Corporation, Cray Research, Digital Equipment Corporation, Hewlett-Packard, Intel, International Business Machines, Silicon Graphics, and Sun Microsystems. The machines are compared by their execution speed, computational accuracy, and porting effort. The results of this study show that the raw computational power needed for real-time simulation is now offered by workstations.

Proficiency performance benchmarks for removal of simulated brain tumors using a virtual reality simulator NeuroTouch.

PubMed

AlZhrani, Gmaan; Alotaibi, Fahad; Azarnoush, Hamed; Winkler-Schwartz, Alexander; Sabbagh, Abdulrahman; Bajunaid, Khalid; Lajoie, Susanne P; Del Maestro, Rolando F

2015-01-01

Assessment of neurosurgical technical skills involved in the resection of cerebral tumors in operative environments is complex. Educators emphasize the need to develop and use objective and meaningful assessment tools that are reliable and valid for assessing trainees' progress in acquiring surgical skills. The purpose of this study was to develop proficiency performance benchmarks for a newly proposed set of objective measures (metrics) of neurosurgical technical skills performance during simulated brain tumor resection using a new virtual reality simulator (NeuroTouch). Each participant performed the resection of 18 simulated brain tumors of different complexity using the NeuroTouch platform. Surgical performance was computed using Tier 1 and Tier 2 metrics derived from NeuroTouch simulator data consisting of (1) safety metrics, including (a) volume of surrounding simulated normal brain tissue removed, (b) sum of forces utilized, and (c) maximum force applied during tumor resection; (2) quality of operation metric, which involved the percentage of tumor removed; and (3) efficiency metrics, including (a) instrument total tip path lengths and (b) frequency of pedal activation. All studies were conducted in the Neurosurgical Simulation Research Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada. A total of 33 participants were recruited, including 17 experts (board-certified neurosurgeons) and 16 novices (7 senior and 9 junior neurosurgery residents). The results demonstrated that "expert" neurosurgeons resected less surrounding simulated normal brain tissue and less tumor tissue than residents. These data are consistent with the concept that "experts" focused more on safety of the surgical procedure compared with novices. By analyzing experts' neurosurgical technical skills performance on these different metrics, we were able to establish benchmarks for goal proficiency performance training of neurosurgery residents. This study furthers our understanding of expert neurosurgical performance during the resection of simulated virtual reality tumors and provides neurosurgical trainees with predefined proficiency performance benchmarks designed to maximize the learning of specific surgical technical skills. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

2018-05-01

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

Time-Dependent Simulations of Turbopump Flows

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan; Chan, William; Williams, Robert

2002-01-01

Unsteady flow simulations for RLV (Reusable Launch Vehicles) 2nd Generation baseline turbopump for one and half impeller rotations have been completed by using a 34.3 Million grid points model. MLP (Multi-Level Parallelism) shared memory parallelism has been implemented in INS3D, and benchmarked. Code optimization for cash based platforms will be completed by the end of September 2001. Moving boundary capability is obtained by using DCF module. Scripting capability from CAD (computer aided design) geometry to solution has been developed. Data compression is applied to reduce data size in post processing. Fluid/Structure coupling has been initiated.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

PubMed

Symonds, C; Kattirtzi, J A; Shalashilin, D V

2018-05-14

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

Time Dependent Simulation of Turbopump Flows

NASA Technical Reports Server (NTRS)

Kiris, Cetin C.; Kwak, Dochan; Chan, William; Williams, Robert

2001-01-01

The objective of this viewgraph presentation is to enhance incompressible flow simulation capability for developing aerospace vehicle components, especially unsteady flow phenomena associated with high speed turbo pumps. Unsteady Space Shuttle Main Engine (SSME)-rig1 1 1/2 rotations are completed for the 34.3 million grid points model. The moving boundary capability is obtained by using the DCF module. MLP shared memory parallelism has been implemented and benchmarked in INS3D. The scripting capability from CAD geometry to solution is developed. Data compression is applied to reduce data size in post processing and fluid/structure coupling is initiated.

LES models for incompressible magnetohydrodynamics derived from the variational multiscale formulation

NASA Astrophysics Data System (ADS)

Sondak, David; Oberai, Assad

2012-10-01

Novel large eddy simulation (LES) models are developed for incompressible magnetohydrodynamics (MHD). These models include the application of the variational multiscale formulation (VMS) of LES to the equations of incompressible MHD, a new residual-based eddy viscosity model (RBEVM,) and a mixed LES model that combines the strengths of both of these models. The new models result in a consistent numerical method that is relatively simple to implement. A dynamic procedure for determining model coefficients is no longer required. The new LES models are tested on a decaying Taylor-Green vortex generalized to MHD and benchmarked against classical and state-of-the art LES turbulence models as well as direct numerical simulations (DNS). These new models are able to account for the essential MHD physics which is demonstrated via comparisons of energy spectra. We also compare the performance of our models to a DNS simulation by A. Pouquet et al., for which the ratio of DNS modes to LES modes is 262,144. Additionally, we extend these models to a finite element setting in which boundary conditions play a role. A classic problem on which we test these models is turbulent channel flow, which in the case of MHD, is called Hartmann flow.

Development and Experimental Benchmark of Simulations to Predict Used Nuclear Fuel Cladding Temperatures during Drying and Transfer Operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greiner, Miles

Radial hydride formation in high-burnup used fuel cladding has the potential to radically reduce its ductility and suitability for long-term storage and eventual transport. To avoid this formation, the maximum post-reactor temperature must remain sufficiently low to limit the cladding hoop stress, and so that hydrogen from the existing circumferential hydrides will not dissolve and become available to re-precipitate into radial hydrides under the slow cooling conditions during drying, transfer and early dry-cask storage. The objective of this research is to develop and experimentallybenchmark computational fluid dynamics simulations of heat transfer in post-pool-storage drying operations, when high-burnup fuel cladding ismore » likely to experience its highest temperature. These benchmarked tools can play a key role in evaluating dry cask storage systems for extended storage of high-burnup fuels and post-storage transportation, including fuel retrievability. The benchmarked tools will be used to aid the design of efficient drying processes, as well as estimate variations of surface temperatures as a means of inferring helium integrity inside the canister or cask. This work will be conducted effectively because the principal investigator has experience developing these types of simulations, and has constructed a test facility that can be used to benchmark them.« less

Benchmark of 3D halo neutral simulation in TRANSP and FIDASIM and application to projected neutral-beam-heated NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Liu, D.; Medley, S. S.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2014-10-01

A cloud of halo neutrals is created in the vicinity of beam footprint during the neutral beam injection and the halo neutral density can be comparable with beam neutral density. Proper modeling of halo neutrals is critical to correctly interpret neutral particle analyzers (NPA) and fast ion D-alpha (FIDA) signals since these signals strongly depend on local beam and halo neutral density. A 3D halo neutral model has been recently developed and implemented inside TRANSP code. The 3D halo neutral code uses a ``beam-in-a-box'' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce thermal halo neutrals that are tracked through successive halo neutral generations until an ionization event occurs or a descendant halo exits the box. A benchmark between 3D halo neural model in TRANSP and in FIDA/NPA synthetic diagnostic code FIDASIM is carried out. Detailed comparison of halo neutral density profiles from two codes will be shown. The NPA and FIDA simulations with and without 3D halos are applied to projections of plasma performance for the National Spherical Tours eXperiment-Upgrade (NSTX-U) and the effects of halo neutral density on NPA and FIDA signal amplitude and profile will be presented. Work supported by US DOE.

RF transient analysis and stabilization of the phase and energy of the proposed PIP-II LINAC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edelen, J. P.; Chase, B. E.

This paper describes a recent effort to develop and benchmark a simulation tool for the analysis of RF transients and their compensation in an H- linear accelerator. Existing tools in this area either focus on electron LINACs or lack fundamental details about the LLRF system that are necessary to provide realistic performance estimates. In our paper we begin with a discussion of our computational models followed by benchmarking with existing beam-dynamics codes and measured data. We then analyze the effect of RF transients and their compensation in the PIP-II LINAC, followed by an analysis of calibration errors and how amore » Newton’s Method based feedback scheme can be used to regulate the beam energy to within the specified limits.« less

PMLB: a large benchmark suite for machine learning evaluation and comparison.

PubMed

Olson, Randal S; La Cava, William; Orzechowski, Patryk; Urbanowicz, Ryan J; Moore, Jason H

2017-01-01

The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists. The present study introduces an accessible, curated, and developing public benchmark resource to facilitate identification of the strengths and weaknesses of different machine learning methodologies. We compare meta-features among the current set of benchmark datasets in this resource to characterize the diversity of available data. Finally, we apply a number of established machine learning methods to the entire benchmark suite and analyze how datasets and algorithms cluster in terms of performance. From this study, we find that existing benchmarks lack the diversity to properly benchmark machine learning algorithms, and there are several gaps in benchmarking problems that still need to be considered. This work represents another important step towards understanding the limitations of popular benchmarking suites and developing a resource that connects existing benchmarking standards to more diverse and efficient standards in the future.

OECD-NEA Expert Group on Multi-Physics Experimental Data, Benchmarks and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valentine, Timothy; Rohatgi, Upendra S.

High-fidelity, multi-physics modeling and simulation (M&S) tools are being developed and utilized for a variety of applications in nuclear science and technology and show great promise in their abilities to reproduce observed phenomena for many applications. Even with the increasing fidelity and sophistication of coupled multi-physics M&S tools, the underpinning models and data still need to be validated against experiments that may require a more complex array of validation data because of the great breadth of the time, energy and spatial domains of the physical phenomena that are being simulated. The Expert Group on Multi-Physics Experimental Data, Benchmarks and Validationmore » (MPEBV) of the Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) was formed to address the challenges with the validation of such tools. The work of the MPEBV expert group is shared among three task forces to fulfill its mandate and specific exercises are being developed to demonstrate validation principles for common industrial challenges. This paper describes the overall mission of the group, the specific objectives of the task forces, the linkages among the task forces, and the development of a validation exercise that focuses on a specific reactor challenge problem.« less

Unsteady Computational Tests of a Non-Equilibrium

NASA Astrophysics Data System (ADS)

Jirasek, Adam; Hamlington, Peter; Lofthouse, Andrew; Usafa Collaboration; Cu Boulder Collaboration

2017-11-01

A non-equilibrium turbulence model is assessed on simulations of three practically-relevant unsteady test cases; oscillating channel flow, transonic flow around an oscillating airfoil, and transonic flow around the Benchmark Super-Critical Wing. The first case is related to piston-driven flows while the remaining cases are relevant to unsteady aerodynamics at high angles of attack and transonic speeds. Non-equilibrium turbulence effects arise in each of these cases in the form of a lag between the mean strain rate and Reynolds stresses, resulting in reduced kinetic energy production compared to classical equilibrium turbulence models that are based on the gradient transport (or Boussinesq) hypothesis. As a result of the improved representation of unsteady flow effects, the non-equilibrium model provides substantially better agreement with available experimental data than do classical equilibrium turbulence models. This suggests that the non-equilibrium model may be ideally suited for simulations of modern high-speed, high angle of attack aerodynamics problems.

Feebates and Fuel Economy Standards: Impacts on Fuel Use in Light-Duty Vehicles and Greenhouse Gas Emissions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greene, David L

2011-01-01

This study evaluates the potential impacts of a national feebate system, a market-based policy that consists of graduated fees on low-fuel-economy (or high-emitting) vehicles and rebates for high-fuel-economy (or lowemitting) vehicles. In their simplest form, feebate systems operate under three conditions: a benchmark divides all vehicles into two categories-those charged fees and those eligible for rebates; the sizes of the fees and rebates are a function of a vehicle's deviation from its benchmark; and placement of the benchmark ensures revenue neutrality or a desired level of subsidy or revenue. A model developed by the University of California for the Californiamore » Air Resources Board was revised and used to estimate the effects of six feebate structures on fuel economy and sales of new light-duty vehicles, given existing and anticipated future fuel economy and emission standards. These estimates for new vehicles were then entered into a vehicle stock model that simulated the evolution of the entire vehicle stock. The results indicate that feebates could produce large, additional reductions in emissions and fuel consumption, in large part by encouraging market acceptance of technologies with advanced fuel economy, such as hybrid electric vehicles.« less

Uncertainty in Earth System Models: Benchmarks for Ocean Model Performance and Validation

NASA Astrophysics Data System (ADS)

Ogunro, O. O.; Elliott, S.; Collier, N.; Wingenter, O. W.; Deal, C.; Fu, W.; Hoffman, F. M.

2017-12-01

The mean ocean CO2 sink is a major component of the global carbon budget, with marine reservoirs holding about fifty times more carbon than the atmosphere. Phytoplankton play a significant role in the net carbon sink through photosynthesis and drawdown, such that about a quarter of anthropogenic CO2 emissions end up in the ocean. Biology greatly increases the efficiency of marine environments in CO2 uptake and ultimately reduces the impact of the persistent rise in atmospheric concentrations. However, a number of challenges remain in appropriate representation of marine biogeochemical processes in Earth System Models (ESM). These threaten to undermine the community effort to quantify seasonal to multidecadal variability in ocean uptake of atmospheric CO2. In a bid to improve analyses of marine contributions to climate-carbon cycle feedbacks, we have developed new analysis methods and biogeochemistry metrics as part of the International Ocean Model Benchmarking (IOMB) effort. Our intent is to meet the growing diagnostic and benchmarking needs of ocean biogeochemistry models. The resulting software package has been employed to validate DOE ocean biogeochemistry results by comparison with observational datasets. Several other international ocean models contributing results to the fifth phase of the Coupled Model Intercomparison Project (CMIP5) were analyzed simultaneously. Our comparisons suggest that the biogeochemical processes determining CO2 entry into the global ocean are not well represented in most ESMs. Polar regions continue to show notable biases in many critical biogeochemical and physical oceanographic variables. Some of these disparities could have first order impacts on the conversion of atmospheric CO2 to organic carbon. In addition, single forcing simulations show that the current ocean state can be partly explained by the uptake of anthropogenic emissions. Combined effects of two or more of these forcings on ocean biogeochemical cycles and ecosystems are challenging to predict since additive or antagonistic effects may occur. A benchmarking tool for accurate assessment and validation of marine biogeochemical outputs will be indispensable as the model community continues to improve ESM developments. It will provide a first order tool in understanding climate-carbon cycle feedbacks.

Seismo-acoustic ray model benchmarking against experimental tank data.

PubMed

Camargo Rodríguez, Orlando; Collis, Jon M; Simpson, Harry J; Ey, Emanuel; Schneiderwind, Joseph; Felisberto, Paulo

2012-08-01

Acoustic predictions of the recently developed traceo ray model, which accounts for bottom shear properties, are benchmarked against tank experimental data from the EPEE-1 and EPEE-2 (Elastic Parabolic Equation Experiment) experiments. Both experiments are representative of signal propagation in a Pekeris-like shallow-water waveguide over a non-flat isotropic elastic bottom, where significant interaction of the signal with the bottom can be expected. The benchmarks show, in particular, that the ray model can be as accurate as a parabolic approximation model benchmarked in similar conditions. The results of benchmarking are important, on one side, as a preliminary experimental validation of the model and, on the other side, demonstrates the reliability of the ray approach for seismo-acoustic applications.

MHD Simulations of Plasma Dynamics with Non-Axisymmetric Boundaries

NASA Astrophysics Data System (ADS)

Hansen, Chris; Levesque, Jeffrey; Morgan, Kyle; Jarboe, Thomas

2015-11-01

The arbitrary geometry, 3D extended MHD code PSI-TET is applied to linear and non-linear simulations of MCF plasmas with non-axisymmetric boundaries. Progress and results from simulations on two experiments will be presented: 1) Detailed validation studies of the HIT-SI experiment with self-consistent modeling of plasma dynamics in the helicity injectors. Results will be compared to experimental data and NIMROD simulations that model the effect of the helicity injectors through boundary conditions on an axisymmetric domain. 2) Linear studies of HBT-EP with different wall configurations focusing on toroidal asymmetries in the adjustable conducting wall. HBT-EP studies the effect of active/passive stabilization with an adjustable ferritic wall. Results from linear verification and benchmark studies of ideal mode growth with and without toroidal asymmetries will be presented and compared to DCON predictions. Simulations of detailed experimental geometries are enabled by use of the PSI-TET code, which employs a high order finite element method on unstructured tetrahedral grids that are generated directly from CAD models. Further development of PSI-TET will also be presented including work to support resistive wall regions within extended MHD simulations. Work supported by DoE.

Validating the simulation of large-scale parallel applications using statistical characteristics

DOE PAGES

Zhang, Deli; Wilke, Jeremiah; Hendry, Gilbert; ...

2016-03-01

Simulation is a widely adopted method to analyze and predict the performance of large-scale parallel applications. Validating the hardware model is highly important for complex simulations with a large number of parameters. Common practice involves calculating the percent error between the projected and the real execution time of a benchmark program. However, in a high-dimensional parameter space, this coarse-grained approach often suffers from parameter insensitivity, which may not be known a priori. Moreover, the traditional approach cannot be applied to the validation of software models, such as application skeletons used in online simulations. In this work, we present a methodologymore » and a toolset for validating both hardware and software models by quantitatively comparing fine-grained statistical characteristics obtained from execution traces. Although statistical information has been used in tasks like performance optimization, this is the first attempt to apply it to simulation validation. Lastly, our experimental results show that the proposed evaluation approach offers significant improvement in fidelity when compared to evaluation using total execution time, and the proposed metrics serve as reliable criteria that progress toward automating the simulation tuning process.« less

UNSAT-H Version 2. 0: Unsaturated soil water and heat flow model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fayer, M.J.; Jones, T.L.

1990-04-01

This report documents UNSAT-H Version 2.0, a model for calculating water and heat flow in unsaturated media. The documentation includes the bases for the conceptual model and its numerical implementation, benchmark test cases, example simulations involving layered soils and plant transpiration, and the code listing. Waste management practices at the Hanford Site have included disposal of low-level wastes by near-surface burial. Predicting the future long-term performance of any such burial site in terms of migration of contaminants requires a model capable of simulating water flow in the unsaturated soils above the buried waste. The model currently used to meet thismore » need is UNSAT-H. This model was developed at Pacific Northwest Laboratory to assess water dynamics of near-surface, waste-disposal sites at the Hanford Site. The code is primarily used to predict deep drainage as a function of such environmental conditions as climate, soil type, and vegetation. UNSAT-H is also used to simulate the effects of various practices to enhance isolation of wastes. 66 refs., 29 figs., 7 tabs.« less

Parallel Algorithms for Monte Carlo Particle Transport Simulation on Exascale Computing Architectures

NASA Astrophysics Data System (ADS)

Romano, Paul Kollath

Monte Carlo particle transport methods are being considered as a viable option for high-fidelity simulation of nuclear reactors. While Monte Carlo methods offer several potential advantages over deterministic methods, there are a number of algorithmic shortcomings that would prevent their immediate adoption for full-core analyses. In this thesis, algorithms are proposed both to ameliorate the degradation in parallel efficiency typically observed for large numbers of processors and to offer a means of decomposing large tally data that will be needed for reactor analysis. A nearest-neighbor fission bank algorithm was proposed and subsequently implemented in the OpenMC Monte Carlo code. A theoretical analysis of the communication pattern shows that the expected cost is O( N ) whereas traditional fission bank algorithms are O(N) at best. The algorithm was tested on two supercomputers, the Intrepid Blue Gene/P and the Titan Cray XK7, and demonstrated nearly linear parallel scaling up to 163,840 processor cores on a full-core benchmark problem. An algorithm for reducing network communication arising from tally reduction was analyzed and implemented in OpenMC. The proposed algorithm groups only particle histories on a single processor into batches for tally purposes---in doing so it prevents all network communication for tallies until the very end of the simulation. The algorithm was tested, again on a full-core benchmark, and shown to reduce network communication substantially. A model was developed to predict the impact of load imbalances on the performance of domain decomposed simulations. The analysis demonstrated that load imbalances in domain decomposed simulations arise from two distinct phenomena: non-uniform particle densities and non-uniform spatial leakage. The dominant performance penalty for domain decomposition was shown to come from these physical effects rather than insufficient network bandwidth or high latency. The model predictions were verified with measured data from simulations in OpenMC on a full-core benchmark problem. Finally, a novel algorithm for decomposing large tally data was proposed, analyzed, and implemented/tested in OpenMC. The algorithm relies on disjoint sets of compute processes and tally servers. The analysis showed that for a range of parameters relevant to LWR analysis, the tally server algorithm should perform with minimal overhead. Tests were performed on Intrepid and Titan and demonstrated that the algorithm did indeed perform well over a wide range of parameters. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

Assessing Discriminative Performance at External Validation of Clinical Prediction Models

PubMed Central

Nieboer, Daan; van der Ploeg, Tjeerd; Steyerberg, Ewout W.

2016-01-01

Introduction External validation studies are essential to study the generalizability of prediction models. Recently a permutation test, focusing on discrimination as quantified by the c-statistic, was proposed to judge whether a prediction model is transportable to a new setting. We aimed to evaluate this test and compare it to previously proposed procedures to judge any changes in c-statistic from development to external validation setting. Methods We compared the use of the permutation test to the use of benchmark values of the c-statistic following from a previously proposed framework to judge transportability of a prediction model. In a simulation study we developed a prediction model with logistic regression on a development set and validated them in the validation set. We concentrated on two scenarios: 1) the case-mix was more heterogeneous and predictor effects were weaker in the validation set compared to the development set, and 2) the case-mix was less heterogeneous in the validation set and predictor effects were identical in the validation and development set. Furthermore we illustrated the methods in a case study using 15 datasets of patients suffering from traumatic brain injury. Results The permutation test indicated that the validation and development set were homogenous in scenario 1 (in almost all simulated samples) and heterogeneous in scenario 2 (in 17%-39% of simulated samples). Previously proposed benchmark values of the c-statistic and the standard deviation of the linear predictors correctly pointed at the more heterogeneous case-mix in scenario 1 and the less heterogeneous case-mix in scenario 2. Conclusion The recently proposed permutation test may provide misleading results when externally validating prediction models in the presence of case-mix differences between the development and validation population. To correctly interpret the c-statistic found at external validation it is crucial to disentangle case-mix differences from incorrect regression coefficients. PMID:26881753

Assessing Discriminative Performance at External Validation of Clinical Prediction Models.

PubMed

Nieboer, Daan; van der Ploeg, Tjeerd; Steyerberg, Ewout W

2016-01-01

External validation studies are essential to study the generalizability of prediction models. Recently a permutation test, focusing on discrimination as quantified by the c-statistic, was proposed to judge whether a prediction model is transportable to a new setting. We aimed to evaluate this test and compare it to previously proposed procedures to judge any changes in c-statistic from development to external validation setting. We compared the use of the permutation test to the use of benchmark values of the c-statistic following from a previously proposed framework to judge transportability of a prediction model. In a simulation study we developed a prediction model with logistic regression on a development set and validated them in the validation set. We concentrated on two scenarios: 1) the case-mix was more heterogeneous and predictor effects were weaker in the validation set compared to the development set, and 2) the case-mix was less heterogeneous in the validation set and predictor effects were identical in the validation and development set. Furthermore we illustrated the methods in a case study using 15 datasets of patients suffering from traumatic brain injury. The permutation test indicated that the validation and development set were homogenous in scenario 1 (in almost all simulated samples) and heterogeneous in scenario 2 (in 17%-39% of simulated samples). Previously proposed benchmark values of the c-statistic and the standard deviation of the linear predictors correctly pointed at the more heterogeneous case-mix in scenario 1 and the less heterogeneous case-mix in scenario 2. The recently proposed permutation test may provide misleading results when externally validating prediction models in the presence of case-mix differences between the development and validation population. To correctly interpret the c-statistic found at external validation it is crucial to disentangle case-mix differences from incorrect regression coefficients.

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

PubMed Central

2014-01-01

Background The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. Results In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. Conclusions A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. PMID:24708189

Evaluating the coupled vegetation-fire model, LPJ-GUESS-SPITFIRE, against observed tropical forest biomass

NASA Astrophysics Data System (ADS)

Spessa, Allan; Forrest, Matthew; Werner, Christian; Steinkamp, Joerg; Hickler, Thomas

2013-04-01

Wildfire is a fundamental Earth System process. It is the most important disturbance worldwide in terms of area and variety of biomes affected; a major mechanism by which carbon is transferred from the land to the atmosphere (2-4 Pg per annum, equiv. 20-30% of global fossil fuel emissions over the last decade); and globally a significant source of particulate aerosols and trace greenhouse gases. Fire is also potentially important as a feedback in the climate system. If climate change favours more intense fire regimes, this would result in a net transfer of carbon from ecosystems to the atmosphere, as well as higher emissions, and under certain circumstances, increased troposphere ozone production- all contributing to positive climate-land surface feedbacks. Quantitative analysis of fire-vegetation-climate interactions has been held back until recently by a lack of consistent global data sets on fire, and by the underdeveloped state of dynamic vegetation-fire modelling. Dynamic vegetation-fire modelling is an essential part of our forecasting armory for examining the possible impacts of climate, fire regimes and land-use on ecosystems and emissions from biomass burning beyond the observation period, as part of future climate or paleo-climate studies. LPJ-GUESS is a process-based model of vegetation dynamics designed for regional to global applications. It combines features of the Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ-DGVM) with those of the General Ecosystem Simulator (GUESS) in a single, flexible modelling framework. The models have identical representations of eco-physiological and biogeochemical processes, including the hydrological cycle. However, they differ in the detail with which vegetation dynamics and canopy structure are simulated. Simplified, computationally efficient representations are used in the LPJ-DGVM, while LPJ-GUESS employs a gap-model approach, which better captures ecological succession and hence ecosystem changes due to disturbance such as fire. SPITFIRE (SPread and InTensity of FIRe and Emissions) mechanistically simulates the number of fires, area burnt, fire intensity, crown fires, fire-induced plant mortality, and emissions of carbon, trace gases and aerosols from biomass burning. Originally developed as an embedded model within LPJ-DGVM, SPITFIRE has since been coupled to LPJ-GUESS. However, neither LPJ-DGVM-SPITFIRE nor LPJ-GUESS-SPITFIRE has been fully benchmarked, especially in terms of how well each model simulates vegetation patterns and biomass in areas where fire is known to be important. This information is crucial if we are to have confidence in the models in forecasting fire, emissions from biomass burning and fire-climate impacts on ecosystems. Here we report on the benchmarking of the LPJ-GUESS-SPITFIRE model. We benchmarked LPJ-GUESS-SPITFIRE driven by a combination of daily reanalysis climate data (Sheffield 2012), monthly GFEDv3 burnt area data (1997-2009) (van der Werf et al. 2010) and long-term annual fire statistics (1901 to 2000) (Mouillot and Field 2005) against new Lidar-based biomass data for tropical forests and savannas (Saatchi et al. 2011; Baccini et al., 2012). Our new work has focused on revising the way GUESS simulates tree allometry, light penetration through the tree canopy and sapling recruitment, and how GUESS-SPITFIRE simulates fire-induced mortality, all based on recent literature, as well as a more explicit accounting of land cover change (JRC's GLC 2009). We present how these combined changes result in a much improved simulation of tree carbon across the tropics, including the Americas, Africa, Asia and Australia. Our results are compared with respect to more empirical-based approaches to calculating emissions from biomass burning. We discuss our findings in terms of improved forecasting of fire, emissions from biomass burning and fire-climate impacts on ecosystems.

Multiscale Modeling of Structurally-Graded Materials Using Discrete Dislocation Plasticity Models and Continuum Crystal Plasticity Models

NASA Technical Reports Server (NTRS)

Saether, Erik; Hochhalter, Jacob D.; Glaessgen, Edward H.

2012-01-01

A multiscale modeling methodology that combines the predictive capability of discrete dislocation plasticity and the computational efficiency of continuum crystal plasticity is developed. Single crystal configurations of different grain sizes modeled with periodic boundary conditions are analyzed using discrete dislocation plasticity (DD) to obtain grain size-dependent stress-strain predictions. These relationships are mapped into crystal plasticity parameters to develop a multiscale DD/CP model for continuum level simulations. A polycrystal model of a structurally-graded microstructure is developed, analyzed and used as a benchmark for comparison between the multiscale DD/CP model and the DD predictions. The multiscale DD/CP model follows the DD predictions closely up to an initial peak stress and then follows a strain hardening path that is parallel but somewhat offset from the DD predictions. The difference is believed to be from a combination of the strain rate in the DD simulation and the inability of the DD/CP model to represent non-monotonic material response.

Evaluation of Offline Models Used to Simulate Components of the Permafrost Carbon Feedback: Experience from the Permafrost Carbon Network Model Integration Group

NASA Astrophysics Data System (ADS)

McGuire, A. D.

2016-12-01

The Model Integration Group of the Permafrost Carbon Network (see http://www.permafrostcarbon.org/) has conducted studies to evaluate the sensitivity of offline terrestrial permafrost and carbon models to both historical and projected climate change. These studies indicate that there is a wide range of (1) initial states permafrost extend and carbon stocks simulated by these models and (2) responses of permafrost extent and carbon stocks to both historical and projected climate change. In this study, we synthesize what has been learned about the variability in initial states among models and the driving factors that contribute to variability in the sensitivity of responses. We conclude the talk with a discussion of efforts needed by (1) the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost carbon feedback and (2) the modeling and observational communities to jointly develop data sets and methodologies to more effectively benchmark models.

Benchmarking of measurement and simulation of transverse rms-emittance growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeon, Dong-O

2008-01-01

Transverse emittance growth along the Alvarez DTL section is a major concern with respect to the preservation of beam quality of high current beams at the GSI UNILAC. In order to define measures to reduce this growth appropriated tools to simulate the beam dynamics are indispensable. This paper is about the benchmarking of three beam dynamics simulation codes, i.e. DYNAMION, PARMILA, and PARTRAN against systematic measurements of beam emittances for different machine settings. Experimental set-ups, data reduction, the preparation of the simulations, and the evaluation of the simulations will be described. It was found that the measured 100%-rmsemittances behind themore » DTL exceed the simulated values. Comparing measured 90%-rms-emittances to the simulated 95%-rms-emittances gives fair to good agreement instead. The sum of horizontal and vertical emittances is even described well by the codes as long as experimental 90%-rmsemittances are compared to simulated 95%-rms-emittances. Finally, the successful reduction of transverse emittance growth by systematic beam matching is reported.« less

Benchmarking monthly homogenization algorithms

NASA Astrophysics Data System (ADS)

Venema, V. K. C.; Mestre, O.; Aguilar, E.; Auer, I.; Guijarro, J. A.; Domonkos, P.; Vertacnik, G.; Szentimrey, T.; Stepanek, P.; Zahradnicek, P.; Viarre, J.; Müller-Westermeier, G.; Lakatos, M.; Williams, C. N.; Menne, M.; Lindau, R.; Rasol, D.; Rustemeier, E.; Kolokythas, K.; Marinova, T.; Andresen, L.; Acquaotta, F.; Fratianni, S.; Cheval, S.; Klancar, M.; Brunetti, M.; Gruber, C.; Prohom Duran, M.; Likso, T.; Esteban, P.; Brandsma, T.

2011-08-01

The COST (European Cooperation in Science and Technology) Action ES0601: Advances in homogenization methods of climate series: an integrated approach (HOME) has executed a blind intercomparison and validation study for monthly homogenization algorithms. Time series of monthly temperature and precipitation were evaluated because of their importance for climate studies and because they represent two important types of statistics (additive and multiplicative). The algorithms were validated against a realistic benchmark dataset. The benchmark contains real inhomogeneous data as well as simulated data with inserted inhomogeneities. Random break-type inhomogeneities were added to the simulated datasets modeled as a Poisson process with normally distributed breakpoint sizes. To approximate real world conditions, breaks were introduced that occur simultaneously in multiple station series within a simulated network of station data. The simulated time series also contained outliers, missing data periods and local station trends. Further, a stochastic nonlinear global (network-wide) trend was added. Participants provided 25 separate homogenized contributions as part of the blind study as well as 22 additional solutions submitted after the details of the imposed inhomogeneities were revealed. These homogenized datasets were assessed by a number of performance metrics including (i) the centered root mean square error relative to the true homogeneous value at various averaging scales, (ii) the error in linear trend estimates and (iii) traditional contingency skill scores. The metrics were computed both using the individual station series as well as the network average regional series. The performance of the contributions depends significantly on the error metric considered. Contingency scores by themselves are not very informative. Although relative homogenization algorithms typically improve the homogeneity of temperature data, only the best ones improve precipitation data. Training was found to be very important. Moreover, state-of-the-art relative homogenization algorithms developed to work with an inhomogeneous reference are shown to perform best. The study showed that currently automatic algorithms can perform as well as manual ones.

Non-parametric identification of multivariable systems: A local rational modeling approach with application to a vibration isolation benchmark

NASA Astrophysics Data System (ADS)

Voorhoeve, Robbert; van der Maas, Annemiek; Oomen, Tom

2018-05-01

Frequency response function (FRF) identification is often used as a basis for control systems design and as a starting point for subsequent parametric system identification. The aim of this paper is to develop a multiple-input multiple-output (MIMO) local parametric modeling approach for FRF identification of lightly damped mechanical systems with improved speed and accuracy. The proposed method is based on local rational models, which can efficiently handle the lightly-damped resonant dynamics. A key aspect herein is the freedom in the multivariable rational model parametrizations. Several choices for such multivariable rational model parametrizations are proposed and investigated. For systems with many inputs and outputs the required number of model parameters can rapidly increase, adversely affecting the performance of the local modeling approach. Therefore, low-order model structures are investigated. The structure of these low-order parametrizations leads to an undesired directionality in the identification problem. To address this, an iterative local rational modeling algorithm is proposed. As a special case recently developed SISO algorithms are recovered. The proposed approach is successfully demonstrated on simulations and on an active vibration isolation system benchmark, confirming good performance of the method using significantly less parameters compared with alternative approaches.

Benchmarking of vertically-integrated CO2 flow simulations at the Sleipner Field, North Sea

NASA Astrophysics Data System (ADS)

Cowton, L. R.; Neufeld, J. A.; White, N. J.; Bickle, M. J.; Williams, G. A.; White, J. C.; Chadwick, R. A.

2018-06-01

Numerical modeling plays an essential role in both identifying and assessing sub-surface reservoirs that might be suitable for future carbon capture and storage projects. Accuracy of flow simulations is tested by benchmarking against historic observations from on-going CO2 injection sites. At the Sleipner project located in the North Sea, a suite of time-lapse seismic reflection surveys enables the three-dimensional distribution of CO2 at the top of the reservoir to be determined as a function of time. Previous attempts have used Darcy flow simulators to model CO2 migration throughout this layer, given the volume of injection with time and the location of the injection point. Due primarily to computational limitations preventing adequate exploration of model parameter space, these simulations usually fail to match the observed distribution of CO2 as a function of space and time. To circumvent these limitations, we develop a vertically-integrated fluid flow simulator that is based upon the theory of topographically controlled, porous gravity currents. This computationally efficient scheme can be used to invert for the spatial distribution of reservoir permeability required to minimize differences between the observed and calculated CO2 distributions. When a uniform reservoir permeability is assumed, inverse modeling is unable to adequately match the migration of CO2 at the top of the reservoir. If, however, the width and permeability of a mapped channel deposit are allowed to independently vary, a satisfactory match between the observed and calculated CO2 distributions is obtained. Finally, the ability of this algorithm to forecast the flow of CO2 at the top of the reservoir is assessed. By dividing the complete set of seismic reflection surveys into training and validation subsets, we find that the spatial pattern of permeability required to match the training subset can successfully predict CO2 migration for the validation subset. This ability suggests that it might be feasible to forecast migration patterns into the future with a degree of confidence. Nevertheless, our analysis highlights the difficulty in estimating reservoir parameters away from the region swept by CO2 without additional observational constraints.

COMPUTERIZED TRAINING OF CRYOSURGERY – A SYSTEM APPROACH

PubMed Central

Keelan, Robert; Yamakawa, Soji; Shimada, Kenji; Rabin, Yoed

2014-01-01

The objective of the current study is to provide the foundation for a computerized training platform for cryosurgery. Consistent with clinical practice, the training process targets the correlation of the frozen region contour with the target region shape, using medical imaging and accepted criteria for clinical success. The current study focuses on system design considerations, including a bioheat transfer model, simulation techniques, optimal cryoprobe layout strategy, and a simulation core framework. Two fundamentally different approaches were considered for the development of a cryosurgery simulator, based on a finite-elements (FE) commercial code (ANSYS) and a proprietary finite-difference (FD) code. Results of this study demonstrate that the FE simulator is superior in terms of geometric modeling, while the FD simulator is superior in terms of runtime. Benchmarking results further indicate that the FD simulator is superior in terms of usage of memory resources, pre-processing, parallel processing, and post-processing. It is envisioned that future integration of a human-interface module and clinical data into the proposed computer framework will make computerized training of cryosurgery a practical reality. PMID:23995400

Upgrades for the CMS simulation

DOE PAGES

Lange, D. J.; Hildreth, M.; Ivantchenko, V. N.; ...

2015-05-22

Over the past several years, the CMS experiment has made significant changes to its detector simulation application. The geometry has been generalized to include modifications being made to the CMS detector for 2015 operations, as well as model improvements to the simulation geometry of the current CMS detector and the implementation of a number of approved and possible future detector configurations. These include both completely new tracker and calorimetry systems. We have completed the transition to Geant4 version 10, we have made significant progress in reducing the CPU resources required to run our Geant4 simulation. These have been achieved throughmore » both technical improvements and through numerical techniques. Substantial speed improvements have been achieved without changing the physics validation benchmarks that the experiment uses to validate our simulation application for use in production. As a result, we will discuss the methods that we implemented and the corresponding demonstrated performance improvements deployed for our 2015 simulation application.« less

Circulation and rainfall climatology of a 10-year (1979 - 1988) integration with the Goddard Laboratory for atmospheres general circulation model

NASA Technical Reports Server (NTRS)

Kim, J.-H.; Sud, Y. C.

1993-01-01

A 10-year (1979-1988) integration of Goddard Laboratory for Atmospheres (GLA) general circulation model (GCM) under Atmospheric Model Intercomparison Project (AMIP) is analyzed and compared with observation. The first momentum fields of circulation variables and also hydrological variables including precipitation, evaporation, and soil moisture are presented. Our goals are (1) to produce a benchmark documentation of the GLA GCM for future model improvements; (2) to examine systematic errors between the simulated and the observed circulation, precipitation, and hydrologic cycle; (3) to examine the interannual variability of the simulated atmosphere and compare it with observation; and (4) to examine the ability of the model to capture the major climate anomalies in response to events such as El Nino and La Nina. The 10-year mean seasonal and annual simulated circulation is quite reasonable compared to the analyzed circulation, except the polar regions and area of high orography. Precipitation over tropics are quite well simulated, and the signal of El Nino/La Nina episodes can be easily identified. The time series of evaporation and soil moisture in the 12 biomes of the biosphere also show reasonable patterns compared to the estimated evaporation and soil moisture.

Monte carlo simulations of the n_TOF lead spallation target with the Geant4 toolkit: A benchmark study

NASA Astrophysics Data System (ADS)

Lerendegui-Marco, J.; Cortés-Giraldo, M. A.; Guerrero, C.; Quesada, J. M.; Meo, S. Lo; Massimi, C.; Barbagallo, M.; Colonna, N.; Mancussi, D.; Mingrone, F.; Sabaté-Gilarte, M.; Vannini, G.; Vlachoudis, V.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bacak, M.; Balibrea, J.; Bečvář, F.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brown, A.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Cortés, G.; Cosentino, L.; Damone, L. A.; Diakaki, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Göbel, K.; Gómez-Hornillos, M. B.; García, A. R.; Gawlik, A.; Gilardoni, S.; Glodariu, T.; Gonçalves, I. F.; González, E.; Griesmayer, E.; Gunsing, F.; Harada, H.; Heinitz, S.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Kalamara, A.; Kavrigin, P.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Kurtulgil, D.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lonsdale, S. J.; Macina, D.; Marganiec, J.; Martínez, T.; Masi, A.; Mastinu, P.; Mastromarco, M.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Musumarra, A.; Negret, A.; Nolte, R.; Oprea, A.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, I.; Praena, J.; Radeck, D.; Rauscher, T.; Reifarth, R.; Rout, P. C.; Rubbia, C.; Ryan, J. A.; Saxena, A.; Schillebeeckx, P.; Schumann, D.; Smith, A. G.; Sosnin, N. V.; Stamatopoulos, A.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tassan-Got, L.; Valenta, S.; Variale, V.; Vaz, P.; Ventura, A.; Vlastou, R.; Wallner, A.; Warren, S.; Woods, P. J.; Wright, T.; Žugec, P.

2017-09-01

Monte Carlo (MC) simulations are an essential tool to determine fundamental features of a neutron beam, such as the neutron flux or the γ-ray background, that sometimes can not be measured or at least not in every position or energy range. Until recently, the most widely used MC codes in this field had been MCNPX and FLUKA. However, the Geant4 toolkit has also become a competitive code for the transport of neutrons after the development of the native Geant4 format for neutron data libraries, G4NDL. In this context, we present the Geant4 simulations of the neutron spallation target of the n_TOF facility at CERN, done with version 10.1.1 of the toolkit. The first goal was the validation of the intra-nuclear cascade models implemented in the code using, as benchmark, the characteristics of the neutron beam measured at the first experimental area (EAR1), especially the neutron flux and energy distribution, and the time distribution of neutrons of equal kinetic energy, the so-called Resolution Function. The second goal was the development of a Monte Carlo tool aimed to provide useful calculations for both the analysis and planning of the upcoming measurements at the new experimental area (EAR2) of the facility.

A comprehensive evaluation of different radiation models in a gas turbine combustor under conditions of oxy-fuel combustion with dry recycle

NASA Astrophysics Data System (ADS)

Kez, V.; Liu, F.; Consalvi, J. L.; Ströhle, J.; Epple, B.

2016-03-01

The oxy-fuel combustion is a promising CO2 capture technology from combustion systems. This process is characterized by much higher CO2 concentrations in the combustion system compared to that of the conventional air-fuel combustion. To accurately predict the enhanced thermal radiation in oxy-fuel combustion, it is essential to take into account the non-gray nature of gas radiation. In this study, radiation heat transfer in a 3D model gas turbine combustor under two test cases at 20 atm total pressure was calculated by various non-gray gas radiation models, including the statistical narrow-band (SNB) model, the statistical narrow-band correlated-k (SNBCK) model, the wide-band correlated-k (WBCK) model, the full spectrum correlated-k (FSCK) model, and several weighted sum of gray gases (WSGG) models. Calculations of SNB, SNBCK, and FSCK were conducted using the updated EM2C SNB model parameters. Results of the SNB model are considered as the benchmark solution to evaluate the accuracy of the other models considered. Results of SNBCK and FSCK are in good agreement with the benchmark solution. The WBCK model is less accurate than SNBCK or FSCK. Considering the three formulations of the WBCK model, the multiple gases formulation is the best choice regarding the accuracy and computational cost. The WSGG model with the parameters of Bordbar et al. (2014) [20] is the most accurate of the three investigated WSGG models. Use of the gray WSSG formulation leads to significant deviations from the benchmark data and should not be applied to predict radiation heat transfer in oxy-fuel combustion systems. A best practice to incorporate the state-of-the-art gas radiation models for high accuracy of radiation heat transfer calculations at minimal increase in computational cost in CFD simulation of oxy-fuel combustion systems for pressure path lengths up to about 10 bar m is suggested.

International land Model Benchmarking (ILAMB) Package v002.00

DOE Data Explorer

Collier, Nathaniel [Oak Ridge National Laboratory; Hoffman, Forrest M. [Oak Ridge National Laboratory; Mu, Mingquan [University of California, Irvine; Randerson, James T. [University of California, Irvine; Riley, William J. [Lawrence Berkeley National Laboratory

2016-05-09

As a contribution to International Land Model Benchmarking (ILAMB) Project, we are providing new analysis approaches, benchmarking tools, and science leadership. The goal of ILAMB is to assess and improve the performance of land models through international cooperation and to inform the design of new measurement campaigns and field studies to reduce uncertainties associated with key biogeochemical processes and feedbacks. ILAMB is expected to be a primary analysis tool for CMIP6 and future model-data intercomparison experiments. This team has developed initial prototype benchmarking systems for ILAMB, which will be improved and extended to include ocean model metrics and diagnostics.

International land Model Benchmarking (ILAMB) Package v001.00

DOE Data Explorer

Mu, Mingquan [University of California, Irvine; Randerson, James T. [University of California, Irvine; Riley, William J. [Lawrence Berkeley National Laboratory; Hoffman, Forrest M. [Oak Ridge National Laboratory

2016-05-02

As a contribution to International Land Model Benchmarking (ILAMB) Project, we are providing new analysis approaches, benchmarking tools, and science leadership. The goal of ILAMB is to assess and improve the performance of land models through international cooperation and to inform the design of new measurement campaigns and field studies to reduce uncertainties associated with key biogeochemical processes and feedbacks. ILAMB is expected to be a primary analysis tool for CMIP6 and future model-data intercomparison experiments. This team has developed initial prototype benchmarking systems for ILAMB, which will be improved and extended to include ocean model metrics and diagnostics.

Models for electricity market efficiency and bidding strategy analysis

NASA Astrophysics Data System (ADS)

Niu, Hui

This dissertation studies models for the analysis of market efficiency and bidding behaviors of market participants in electricity markets. Simulation models are developed to estimate how transmission and operational constraints affect the competitive benchmark and market prices based on submitted bids. This research contributes to the literature in three aspects. First, transmission and operational constraints, which have been neglected in most empirical literature, are considered in the competitive benchmark estimation model. Second, the effects of operational and transmission constraints on market prices are estimated through two models based on the submitted bids of market participants. Third, these models are applied to analyze the efficiency of the Electric Reliability Council Of Texas (ERCOT) real-time energy market by simulating its operations for the time period from January 2002 to April 2003. The characteristics and available information for the ERCOT market are considered. In electricity markets, electric firms compete through both spot market bidding and bilateral contract trading. A linear asymmetric supply function equilibrium (SFE) model with transmission constraints is proposed in this dissertation to analyze the bidding strategies with forward contracts. The research contributes to the literature in several aspects. First, we combine forward contracts, transmission constraints, and multi-period strategy (an obligation for firms to bid consistently over an extended time horizon such as a day or an hour) into the linear asymmetric supply function equilibrium framework. As an ex-ante model, it can provide qualitative insights into firms' behaviors. Second, the bidding strategies related to Transmission Congestion Rights (TCRs) are discussed by interpreting TCRs as linear combination of forwards. Third, the model is a general one in the sense that there is no limitation on the number of firms and scale of the transmission network, which can have asymmetric linear marginal cost structures. In addition to theoretical analysis, we apply our model to simulate the ERCOT real-time market from January 2002 to April 2003. The effects of forward contracts on the ERCOT market are evaluated through the results. It is shown that the model is able to capture features of bidding behavior in the market.

Block matching and Wiener filtering approach to optical turbulence mitigation and its application to simulated and real imagery with quantitative error analysis

NASA Astrophysics Data System (ADS)

Hardie, Russell C.; Rucci, Michael A.; Dapore, Alexander J.; Karch, Barry K.

2017-07-01

We present a block-matching and Wiener filtering approach to atmospheric turbulence mitigation for long-range imaging of extended scenes. We evaluate the proposed method, along with some benchmark methods, using simulated and real-image sequences. The simulated data are generated with a simulation tool developed by one of the authors. These data provide objective truth and allow for quantitative error analysis. The proposed turbulence mitigation method takes a sequence of short-exposure frames of a static scene and outputs a single restored image. A block-matching registration algorithm is used to provide geometric correction for each of the individual input frames. The registered frames are then averaged, and the average image is processed with a Wiener filter to provide deconvolution. An important aspect of the proposed method lies in how we model the degradation point spread function (PSF) for the purposes of Wiener filtering. We use a parametric model that takes into account the level of geometric correction achieved during image registration. This is unlike any method we are aware of in the literature. By matching the PSF to the level of registration in this way, the Wiener filter is able to fully exploit the reduced blurring achieved by registration. We also describe a method for estimating the atmospheric coherence diameter (or Fried parameter) from the estimated motion vectors. We provide a detailed performance analysis that illustrates how the key tuning parameters impact system performance. The proposed method is relatively simple computationally, yet it has excellent performance in comparison with state-of-the-art benchmark methods in our study.

Preliminary Results for the OECD/NEA Time Dependent Benchmark using Rattlesnake, Rattlesnake-IQS and TDKENO

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeHart, Mark D.; Mausolff, Zander; Weems, Zach

2016-08-01

One goal of the MAMMOTH M&S project is to validate the analysis capabilities within MAMMOTH. Historical data has shown limited value for validation of full three-dimensional (3D) multi-physics methods. Initial analysis considered the TREAT startup minimum critical core and one of the startup transient tests. At present, validation is focusing on measurements taken during the M8CAL test calibration series. These exercises will valuable in preliminary assessment of the ability of MAMMOTH to perform coupled multi-physics calculations; calculations performed to date are being used to validate the neutron transport solver Rattlesnake\\cite{Rattlesnake} and the fuels performance code BISON. Other validation projects outsidemore » of TREAT are available for single-physics benchmarking. Because the transient solution capability of Rattlesnake is one of the key attributes that makes it unique for TREAT transient simulations, validation of the transient solution of Rattlesnake using other time dependent kinetics benchmarks has considerable value. The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has recently developed a computational benchmark for transient simulations. This benchmark considered both two-dimensional (2D) and 3D configurations for a total number of 26 different transients. All are negative reactivity insertions, typically returning to the critical state after some time.« less

Study of blood flow in several benchmark micro-channels using a two-fluid approach

PubMed Central

Wu, Wei-Tao; Yang, Fang; Antaki, James F.; Aubry, Nadine; Massoudi, Mehrdad

2015-01-01

It is known that in a vessel whose characteristic dimension (e.g., its diameter) is in the range of 20 to 500 microns, blood behaves as a non-Newtonian fluid, exhibiting complex phenomena, such as shear-thinning, stress relaxation, and also multi-component behaviors, such as the Fahraeus effect, plasma-skimming, etc. For describing these non-Newtonian and multi-component characteristics of blood, using the framework of mixture theory, a two-fluid model is applied, where the plasma is treated as a Newtonian fluid and the red blood cells (RBCs) are treated as shear-thinning fluid. A computational fluid dynamic (CFD) simulation incorporating the constitutive model was implemented using OpenFOAM® in which benchmark problems including a sudden expansion and various driven slots and crevices were studied numerically. The numerical results exhibited good agreement with the experimental observations with respect to both the velocity field and the volume fraction distribution of RBCs. PMID:26240438

Targeting the affordability of cigarettes: a new benchmark for taxation policy in low-income and-middle-income countries.

PubMed

Blecher, Evan

2010-08-01

To investigate the appropriateness of tax incidence (the percentage of the retail price occupied by taxes) benchmarking in low-income and-middle-income countries (LMICs) with rapidly growing economies and to explore the viability of an alternative tax policy rule based on the affordability of cigarettes. The paper outlines criticisms of tax incidence benchmarking, particularly in the context of LMICs. It then considers an affordability-based benchmark using relative income price (RIP) as a measure of affordability. The RIP measures the percentage of annual per capita GDP required to purchase 100 packs of cigarettes. Using South Africa as a case study of an LMIC, future consumption is simulated using both tax incidence benchmarks and affordability benchmarks. I show that a tax incidence benchmark is not an optimal policy tool in South Africa and that an affordability benchmark could be a more effective means of reducing tobacco consumption in the future. Although a tax incidence benchmark was successful in increasing prices and reducing tobacco consumption in South Africa in the past, this approach has drawbacks, particularly in the context of a rapidly growing LMIC economy. An affordability benchmark represents an appropriate alternative that would be more effective in reducing future cigarette consumption.

Current modeling practice may lead to falsely high benchmark dose estimates.

PubMed

Ringblom, Joakim; Johanson, Gunnar; Öberg, Mattias

2014-07-01

Benchmark dose (BMD) modeling is increasingly used as the preferred approach to define the point-of-departure for health risk assessment of chemicals. As data are inherently variable, there is always a risk to select a model that defines a lower confidence bound of the BMD (BMDL) that, contrary to expected, exceeds the true BMD. The aim of this study was to investigate how often and under what circumstances such anomalies occur under current modeling practice. Continuous data were generated from a realistic dose-effect curve by Monte Carlo simulations using four dose groups and a set of five different dose placement scenarios, group sizes between 5 and 50 animals and coefficients of variations of 5-15%. The BMD calculations were conducted using nested exponential models, as most BMD software use nested approaches. "Non-protective" BMDLs (higher than true BMD) were frequently observed, in some scenarios reaching 80%. The phenomenon was mainly related to the selection of the non-sigmoidal exponential model (Effect=a·e(b)(·dose)). In conclusion, non-sigmoid models should be used with caution as it may underestimate the risk, illustrating that awareness of the model selection process and sound identification of the point-of-departure is vital for health risk assessment. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Chemically Realistic Tetrahedral Lattice Models for Polymer Chains: Application to Polyethylene Oxide.

PubMed

Dietschreit, Johannes C B; Diestler, Dennis J; Knapp, Ernst W

2016-05-10

To speed up the generation of an ensemble of poly(ethylene oxide) (PEO) polymer chains in solution, a tetrahedral lattice model possessing the appropriate bond angles is used. The distance between noncovalently bonded atoms is maintained at realistic values by generating chains with an enhanced degree of self-avoidance by a very efficient Monte Carlo (MC) algorithm. Potential energy parameters characterizing this lattice model are adjusted so as to mimic realistic PEO polymer chains in water simulated by molecular dynamics (MD), which serves as a benchmark. The MD data show that PEO chains have a fractal dimension of about two, in contrast to self-avoiding walk lattice models, which exhibit the fractal dimension of 1.7. The potential energy accounts for a mild hydrophobic effect (HYEF) of PEO and for a proper setting of the distribution between trans and gauche conformers. The potential energy parameters are determined by matching the Flory radius, the radius of gyration, and the fraction of trans torsion angles in the chain. A gratifying result is the excellent agreement of the pair distribution function and the angular correlation for the lattice model with the benchmark distribution. The lattice model allows for the precise computation of the torsional entropy of the chain. The generation of polymer conformations of the adjusted lattice model is at least 2 orders of magnitude more efficient than MD simulations of the PEO chain in explicit water. This method of generating chain conformations on a tetrahedral lattice can also be applied to other types of polymers with appropriate adjustment of the potential energy function. The efficient MC algorithm for generating chain conformations on a tetrahedral lattice is available for download at https://github.com/Roulattice/Roulattice .

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnamurthy, Dheepak

This paper is an overview of Power System Simulation Toolbox (psst). psst is an open-source Python application for the simulation and analysis of power system models. psst simulates the wholesale market operation by solving a DC Optimal Power Flow (DCOPF), Security Constrained Unit Commitment (SCUC) and a Security Constrained Economic Dispatch (SCED). psst also includes models for the various entities in a power system such as Generator Companies (GenCos), Load Serving Entities (LSEs) and an Independent System Operator (ISO). psst features an open modular object oriented architecture that will make it useful for researchers to customize, expand, experiment beyond solvingmore » traditional problems. psst also includes a web based Graphical User Interface (GUI) that allows for user friendly interaction and for implementation on remote High Performance Computing (HPCs) clusters for parallelized operations. This paper also provides an illustrative application of psst and benchmarks with standard IEEE test cases to show the advanced features and the performance of toolbox.« less

Benchmark Simulation of Natural Circulation Cooling System with Salt Working Fluid Using SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, K. K.; Scarlat, R. O.; Hu, R.

Liquid salt-cooled reactors, such as the Fluoride Salt-Cooled High-Temperature Reactor (FHR), offer passive decay heat removal through natural circulation using Direct Reactor Auxiliary Cooling System (DRACS) loops. The behavior of such systems should be well-understood through performance analysis. The advanced system thermal-hydraulics tool System Analysis Module (SAM) from Argonne National Laboratory has been selected for this purpose. The work presented here is part of a larger study in which SAM modeling capabilities are being enhanced for the system analyses of FHR or Molten Salt Reactors (MSR). Liquid salt thermophysical properties have been implemented in SAM, as well as properties ofmore » Dowtherm A, which is used as a simulant fluid for scaled experiments, for future code validation studies. Additional physics modules to represent phenomena specific to salt-cooled reactors, such as freezing of coolant, are being implemented in SAM. This study presents a useful first benchmark for the applicability of SAM to liquid salt-cooled reactors: it provides steady-state and transient comparisons for a salt reactor system. A RELAP5-3D model of the Mark-1 Pebble-Bed FHR (Mk1 PB-FHR), and in particular its DRACS loop for emergency heat removal, provides steady state and transient results for flow rates and temperatures in the system that are used here for code-to-code comparison with SAM. The transient studied is a loss of forced circulation with SCRAM event. To the knowledge of the authors, this is the first application of SAM to FHR or any other molten salt reactors. While building these models in SAM, any gaps in the code’s capability to simulate such systems are identified and addressed immediately, or listed as future improvements to the code.« less

First benchmark of the Unstructured Grid Adaptation Working Group

NASA Technical Reports Server (NTRS)

Ibanez, Daniel; Barral, Nicolas; Krakos, Joshua; Loseille, Adrien; Michal, Todd; Park, Mike

2017-01-01

Unstructured grid adaptation is a technology that holds the potential to improve the automation and accuracy of computational fluid dynamics and other computational disciplines. Difficulty producing the highly anisotropic elements necessary for simulation on complex curved geometries that satisfies a resolution request has limited this technology's widespread adoption. The Unstructured Grid Adaptation Working Group is an open gathering of researchers working on adapting simplicial meshes to conform to a metric field. Current members span a wide range of institutions including academia, industry, and national laboratories. The purpose of this group is to create a common basis for understanding and improving mesh adaptation. We present our first major contribution: a common set of benchmark cases, including input meshes and analytic metric specifications, that are publicly available to be used for evaluating any mesh adaptation code. We also present the results of several existing codes on these benchmark cases, to illustrate their utility in identifying key challenges common to all codes and important differences between available codes. Future directions are defined to expand this benchmark to mature the technology necessary to impact practical simulation workflows.

Comparing Hospital Processes and Outcomes in California Medicare Beneficiaries: Simulation Prompts Reconsideration.

PubMed

Escobar, Gabriel J; Baker, Jennifer M; Turk, Benjamin J; Draper, David; Liu, Vincent; Kipnis, Patricia

2017-01-01

This article is not a traditional research report. It describes how conducting a specific set of benchmarking analyses led us to broader reflections on hospital benchmarking. We reexamined an issue that has received far less attention from researchers than in the past: How variations in the hospital admission threshold might affect hospital rankings. Considering this threshold made us reconsider what benchmarking is and what future benchmarking studies might be like. Although we recognize that some of our assertions are speculative, they are based on our reading of the literature and previous and ongoing data analyses being conducted in our research unit. We describe the benchmarking analyses that led to these reflections. The Centers for Medicare and Medicaid Services' Hospital Compare Web site includes data on fee-for-service Medicare beneficiaries but does not control for severity of illness, which requires physiologic data now available in most electronic medical records.To address this limitation, we compared hospital processes and outcomes among Kaiser Permanente Northern California's (KPNC) Medicare Advantage beneficiaries and non-KPNC California Medicare beneficiaries between 2009 and 2010. We assigned a simulated severity of illness measure to each record and explored the effect of having the additional information on outcomes. We found that if the admission severity of illness in non-KPNC hospitals increased, KPNC hospitals' mortality performance would appear worse; conversely, if admission severity at non-KPNC hospitals' decreased, KPNC hospitals' performance would appear better. Future hospital benchmarking should consider the impact of variation in admission thresholds.

Mathematical simulations of photon interactions using Monte Carlo analysis to evaluate the uncertainty associated with in vivo K X-ray fluorescence measurements of stable lead in bone

NASA Astrophysics Data System (ADS)

Lodwick, Camille J.

This research utilized Monte Carlo N-Particle version 4C (MCNP4C) to simulate K X-ray fluorescent (K XRF) measurements of stable lead in bone. Simulations were performed to investigate the effects that overlying tissue thickness, bone-calcium content, and shape of the calibration standard have on detector response in XRF measurements at the human tibia. Additional simulations of a knee phantom considered uncertainty associated with rotation about the patella during XRF measurements. Simulations tallied the distribution of energy deposited in a high-purity germanium detector originating from collimated 88 keV 109Cd photons in backscatter geometry. Benchmark measurements were performed on simple and anthropometric XRF calibration phantoms of the human leg and knee developed at the University of Cincinnati with materials proven to exhibit radiological characteristics equivalent to human tissue and bone. Initial benchmark comparisons revealed that MCNP4C limits coherent scatter of photons to six inverse angstroms of momentum transfer and a Modified MCNP4C was developed to circumvent the limitation. Subsequent benchmark measurements demonstrated that Modified MCNP4C adequately models photon interactions associated with in vivo K XRF of lead in bone. Further simulations of a simple leg geometry possessing tissue thicknesses from 0 to 10 mm revealed increasing overlying tissue thickness from 5 to 10 mm reduced predicted lead concentrations an average 1.15% per 1 mm increase in tissue thickness (p < 0.0001). An anthropometric leg phantom was mathematically defined in MCNP to more accurately reflect the human form. A simulated one percent increase in calcium content (by mass) of the anthropometric leg phantom's cortical bone demonstrated to significantly reduce the K XRF normalized ratio by 4.5% (p < 0.0001). Comparison of the simple and anthropometric calibration phantoms also suggested that cylindrical calibration standards can underestimate lead content of a human leg up to 4%. The patellar bone structure in which the fluorescent photons originate was found to vary dramatically with measurement angle. The relative contribution of lead signal from the patella declined from 65% to 27% when rotated 30°. However, rotation of the source-detector about the patella from 0 to 45° demonstrated no significant effect on the net K XRF response at the knee.

Benchmarking polarizable molecular dynamics simulations of aqueous sodium hydroxide by diffraction measurements.

PubMed

Vácha, Robert; Megyes, Tunde; Bakó, Imre; Pusztai, László; Jungwirth, Pavel

2009-04-23

Results from molecular dynamics simulations of aqueous hydroxide of varying concentrations have been compared with experimental structural data. First, the polarizable POL3 model was verified against neutron scattering using a reverse Monte Carlo fitting procedure. It was found to be competitive with other simple water models and well suited for combining with hydroxide ions. Second, a set of four polarizable models of OH- were developed by fitting against accurate ab initio calculations for small hydroxide-water clusters. All of these models were found to provide similar results that robustly agree with structural data from X-ray scattering. The present force field thus represents a significant improvement over previously tested nonpolarizable potentials. Although it cannot in principle capture proton hopping and can only approximately describe the charge delocalization within the immediate solvent shell around OH-, it provides structural data that are almost entirely consistent with data obtained from scattering experiments.

Spreading of correlations in the Falicov-Kimball model

NASA Astrophysics Data System (ADS)

Herrmann, Andreas J.; Antipov, Andrey E.; Werner, Philipp

2018-04-01

We study dynamical properties of the one- and two-dimensional Falicov-Kimball model using lattice Monte Carlo simulations. In particular, we calculate the spreading of charge correlations in the equilibrium model and after an interaction quench. The results show a reduction of the light-cone velocity with interaction strength at low temperature, while the phase velocity increases. At higher temperature, the initial spreading is determined by the Fermi velocity of the noninteracting system and the maximum range of the correlations decreases with increasing interaction strength. Charge order correlations in the disorder potential enhance the range of the correlations. We also use the numerically exact lattice Monte Carlo results to benchmark the accuracy of equilibrium and nonequilibrium dynamical cluster approximation calculations. It is shown that the bias introduced by the mapping to a periodized cluster is substantial, and that from a numerical point of view, it is more efficient to simulate the lattice model directly.

Summary of FY15 results of benchmark modeling activities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arguello, J. Guadalupe

2015-08-01

Sandia is participating in the third phase of an is a contributing partner to a U.S.-German "Joint Project" entitled "Comparison of current constitutive models and simulation procedures on the basis of model calculations of the thermo-mechanical behavior and healing of rock salt." The first goal of the project is to check the ability of numerical modeling tools to correctly describe the relevant deformation phenomena in rock salt under various influences. Achieving this goal will lead to increased confidence in the results of numerical simulations related to the secure storage of radioactive wastes in rock salt, thereby enhancing the acceptance ofmore » the results. These results may ultimately be used to make various assertions regarding both the stability analysis of an underground repository in salt, during the operating phase, and the long-term integrity of the geological barrier against the release of harmful substances into the biosphere, in the post-operating phase.« less

Lattice Boltzmann model for three-phase viscoelastic fluid flow

NASA Astrophysics Data System (ADS)

Xie, Chiyu; Lei, Wenhai; Wang, Moran

2018-02-01

A lattice Boltzmann (LB) framework is developed for simulation of three-phase viscoelastic fluid flows in complex geometries. This model is based on a Rothman-Keller type model for immiscible multiphase flows which ensures mass conservation of each component in porous media even for a high density ratio. To account for the viscoelastic effects, the Maxwell constitutive relation is correctly introduced into the momentum equation, which leads to a modified lattice Boltzmann evolution equation for Maxwell fluids by removing the normal but excess viscous term. Our simulation tests indicate that this excess viscous term may induce significant errors. After three benchmark cases, the displacement processes of oil by dispersed polymer are studied as a typical example of three-phase viscoelastic fluid flow. The results show that increasing either the polymer intrinsic viscosity or the elastic modulus will enhance the oil recovery.

Multi-scale simulations of droplets in generic time-dependent flows

NASA Astrophysics Data System (ADS)

Milan, Felix; Biferale, Luca; Sbragaglia, Mauro; Toschi, Federico

2017-11-01

We study the deformation and dynamics of droplets in time-dependent flows using a diffuse interface model for two immiscible fluids. The numerical simulations are at first benchmarked against analytical results of steady droplet deformation, and further extended to the more interesting case of time-dependent flows. The results of these time-dependent numerical simulations are compared against analytical models available in the literature, which assume the droplet shape to be an ellipsoid at all times, with time-dependent major and minor axis. In particular we investigate the time-dependent deformation of a confined droplet in an oscillating Couette flow for the entire capillary range until droplet break-up. In this way these multi component simulations prove to be a useful tool to establish from ``first principles'' the dynamics of droplets in complex flows involving multiple scales. European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No 642069. & European Research Council under the European Community's Seventh Framework Program, ERC Grant Agreement No 339032.

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

PubMed Central

Stephens, Zachary D.; Hudson, Matthew E.; Mainzer, Liudmila S.; Taschuk, Morgan; Weber, Matthew R.; Iyer, Ravishankar K.

2016-01-01

An obstacle to validating and benchmarking methods for genome analysis is that there are few reference datasets available for which the “ground truth” about the mutational landscape of the sample genome is known and fully validated. Additionally, the free and public availability of real human genome datasets is incompatible with the preservation of donor privacy. In order to better analyze and understand genomic data, we need test datasets that model all variants, reflecting known biology as well as sequencing artifacts. Read simulators can fulfill this requirement, but are often criticized for limited resemblance to true data and overall inflexibility. We present NEAT (NExt-generation sequencing Analysis Toolkit), a set of tools that not only includes an easy-to-use read simulator, but also scripts to facilitate variant comparison and tool evaluation. NEAT has a wide variety of tunable parameters which can be set manually on the default model or parameterized using real datasets. The software is freely available at github.com/zstephens/neat-genreads. PMID:27893777

Convection Effects During Bulk Transparent Alloy Solidification in DECLIC-DSI and Phase-Field Simulations in Diffusive Conditions

NASA Astrophysics Data System (ADS)

Mota, F. L.; Song, Y.; Pereda, J.; Billia, B.; Tourret, D.; Debierre, J.-M.; Trivedi, R.; Karma, A.; Bergeon, N.

2017-08-01

To study the dynamical formation and evolution of cellular and dendritic arrays under diffusive growth conditions, three-dimensional (3D) directional solidification experiments were conducted in microgravity on a model transparent alloy onboard the International Space Station using the Directional Solidification Insert in the DEvice for the study of Critical LIquids and Crystallization. Selected experiments were repeated on Earth under gravity-driven fluid flow to evidence convection effects. Both radial and axial macrosegregation resulting from convection are observed in ground experiments, and primary spacings measured on Earth and microgravity experiments are noticeably different. The microgravity experiments provide unique benchmark data for numerical simulations of spatially extended pattern formation under diffusive growth conditions. The results of 3D phase-field simulations highlight the importance of accurately modeling thermal conditions that strongly influence the front recoil of the interface and the selection of the primary spacing. The modeling predictions are in good quantitative agreements with the microgravity experiments.

Study on effective thermal conductivity of silicone/phosphor composite and its size effect by Lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Li, Lan; Zheng, Huai; Yuan, Chao; Hu, Run; Luo, Xiaobing

2016-12-01

The silicone/phosphor composite is widely used in light emitting diode (LED) packaging. The composite thermal properties, especially the effective thermal conductivity, strongly influence the LED performance. In this paper, a lattice Boltzmann model was presented to predict the silicone/phosphor composite effective thermal conductivity. Based on the present lattice Boltzmann model, a random generation method was established to describe the phosphor particle distribution in composite. Benchmarks were conducted by comparing the simulation results with theoretical solutions for simple cases. Then the model was applied to analyze the effective thermal conductivity of the silicone/phosphor composite and its size effect. The deviations between simulation and experimental results are <7 %, when the phosphor volume fraction varies from 0.038 to 0.45. The simulation results also indicate that effective thermal conductivity of the composite with larger particles is higher than that with small particles at the same volume fraction. While mixing these two sizes of phosphor particles provides an extra enhancement for the effective thermal conductivity.

Large historical growth in global terrestrial gross primary production

DOE PAGES

Campbell, J. E.; Berry, J. A.; Seibt, U.; ...

2017-04-05

Growth in terrestrial gross primary production (GPP) may provide a negative feedback for climate change. It remains uncertain, however, to what extent biogeochemical processes can suppress global GPP growth. In consequence, model estimates of terrestrial carbon storage and carbon cycle –climate feedbacks remain poorly constrained. Here we present a global, measurement-based estimate of GPP growth during the twentieth century based on long-term atmospheric carbonyl sulphide (COS) records derived from ice core, firn, and ambient air samples. Here, we interpret these records using a model that simulates changes in COS concentration due to changes in its sources and sinks, including amore » large sink that is related to GPP. We find that the COS record is most consistent with climate-carbon cycle model simulations that assume large GPP growth during the twentieth century (31% ± 5%; mean ± 95% confidence interval). Finally, while this COS analysis does not directly constrain estimates of future GPP growth it provides a global-scale benchmark for historical carbon cycle simulations.« less

Large historical growth in global terrestrial gross primary production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, J. E.; Berry, J. A.; Seibt, U.

Growth in terrestrial gross primary production (GPP) may provide a negative feedback for climate change. It remains uncertain, however, to what extent biogeochemical processes can suppress global GPP growth. In consequence, model estimates of terrestrial carbon storage and carbon cycle –climate feedbacks remain poorly constrained. Here we present a global, measurement-based estimate of GPP growth during the twentieth century based on long-term atmospheric carbonyl sulphide (COS) records derived from ice core, firn, and ambient air samples. Here, we interpret these records using a model that simulates changes in COS concentration due to changes in its sources and sinks, including amore » large sink that is related to GPP. We find that the COS record is most consistent with climate-carbon cycle model simulations that assume large GPP growth during the twentieth century (31% ± 5%; mean ± 95% confidence interval). Finally, while this COS analysis does not directly constrain estimates of future GPP growth it provides a global-scale benchmark for historical carbon cycle simulations.« less

Benchmark levels for the consumptive water footprint of crop production for different environmental conditions: a case study for winter wheat in China

NASA Astrophysics Data System (ADS)

Zhuo, La; Mekonnen, Mesfin M.; Hoekstra, Arjen Y.

2016-11-01

Meeting growing food demands while simultaneously shrinking the water footprint (WF) of agricultural production is one of the greatest societal challenges. Benchmarks for the WF of crop production can serve as a reference and be helpful in setting WF reduction targets. The consumptive WF of crops, the consumption of rainwater stored in the soil (green WF), and the consumption of irrigation water (blue WF) over the crop growing period varies spatially and temporally depending on environmental factors like climate and soil. The study explores which environmental factors should be distinguished when determining benchmark levels for the consumptive WF of crops. Hereto we determine benchmark levels for the consumptive WF of winter wheat production in China for all separate years in the period 1961-2008, for rain-fed vs. irrigated croplands, for wet vs. dry years, for warm vs. cold years, for four different soil classes, and for two different climate zones. We simulate consumptive WFs of winter wheat production with the crop water productivity model AquaCrop at a 5 by 5 arcmin resolution, accounting for water stress only. The results show that (i) benchmark levels determined for individual years for the country as a whole remain within a range of ±20 % around long-term mean levels over 1961-2008, (ii) the WF benchmarks for irrigated winter wheat are 8-10 % larger than those for rain-fed winter wheat, (iii) WF benchmarks for wet years are 1-3 % smaller than for dry years, (iv) WF benchmarks for warm years are 7-8 % smaller than for cold years, (v) WF benchmarks differ by about 10-12 % across different soil texture classes, and (vi) WF benchmarks for the humid zone are 26-31 % smaller than for the arid zone, which has relatively higher reference evapotranspiration in general and lower yields in rain-fed fields. We conclude that when determining benchmark levels for the consumptive WF of a crop, it is useful to primarily distinguish between different climate zones. If actual consumptive WFs of winter wheat throughout China were reduced to the benchmark levels set by the best 25 % of Chinese winter wheat production (1224 m3 t-1 for arid areas and 841 m3 t-1 for humid areas), the water saving in an average year would be 53 % of the current water consumption at winter wheat fields in China. The majority of the yield increase and associated improvement in water productivity can be achieved in southern China.

Modeling of the T S D E Heater Test to Investigate Crushed Salt Reconsolidation and Rock Salt Creep for the Underground Disposal of High-Level Nuclear Waste

NASA Astrophysics Data System (ADS)

Blanco Martin, L.; Rutqvist, J.; Birkholzer, J. T.; Wolters, R.; Lux, K. H.

2014-12-01

Rock salt is a potential medium for the underground disposal of nuclear waste because it has several assets, in particular its water and gas tightness in the undisturbed state, its ability to heal induced fractures and its high thermal conductivity as compared to other shallow-crustal rocks. In addition, the run-of-mine, granular salt, may be used to backfill the mined open spaces. We present simulation results associated with coupled thermal, hydraulic and mechanical processes in the TSDE (Thermal Simulation for Drift Emplacement) experiment, conducted in the Asse salt mine in Germany [1]. During this unique test, conceived to simulate reference repository conditions for spent nuclear fuel, a significant amount of data (temperature, stress changes and displacements, among others) was measured at 20 cross-sections, distributed in two drifts in which a total of six electrical heaters were emplaced. The drifts were subsequently backfilled with crushed salt. This test has been modeled in three-dimensions, using two sequential simulators for flow (mass and heat) and geomechanics, TOUGH-FLAC and FLAC-TOUGH [2]. These simulators have recently been updated to accommodate large strains and time-dependent rheology. The numerical predictions obtained by the two simulators are compared within the framework of an international benchmark exercise, and also with experimental data. Subsequently, a re-calibration of some parameters has been performed. Modeling coupled processes in saliniferous media for nuclear waste disposal is a novel approach, and in this study it has led to the determination of some creep parameters that are very difficult to assess at the laboratory-scale because they require extremely low strain rates. Moreover, the results from the benchmark are very satisfactory and validate the capabilities of the two simulators used to study coupled thermal, mechanical and hydraulic (multi-component, multi-phase) processes relative to the underground disposal of high-level nuclear waste in rock salt. References: [1] Bechthold et al., 1999. BAMBUS-I Project. Euratom, Report EUR19124-EN. [2] Blanco Martín et al., 2014. Comparison of two sequential simulators to investigate thermal-hydraulic-mechanical processes related to nuclear waste isolation in saliniferous formations. In preparation.

Ultracool dwarf benchmarks with Gaia primaries

NASA Astrophysics Data System (ADS)

Marocco, F.; Pinfield, D. J.; Cook, N. J.; Zapatero Osorio, M. R.; Montes, D.; Caballero, J. A.; Gálvez-Ortiz, M. C.; Gromadzki, M.; Jones, H. R. A.; Kurtev, R.; Smart, R. L.; Zhang, Z.; Cabrera Lavers, A. L.; García Álvarez, D.; Qi, Z. X.; Rickard, M. J.; Dover, L.

2017-10-01

We explore the potential of Gaia for the field of benchmark ultracool/brown dwarf companions, and present the results of an initial search for metal-rich/metal-poor systems. A simulated population of resolved ultracool dwarf companions to Gaia primary stars is generated and assessed. Of the order of ˜24 000 companions should be identifiable outside of the Galactic plane (|b| > 10 deg) with large-scale ground- and space-based surveys including late M, L, T and Y types. Our simulated companion parameter space covers 0.02 ≤ M/M⊙ ≤ 0.1, 0.1 ≤ age/Gyr ≤ 14 and -2.5 ≤ [Fe/H] ≤ 0.5, with systems required to have a false alarm probability <10-4, based on projected separation and expected constraints on common distance, common proper motion and/or common radial velocity. Within this bulk population, we identify smaller target subsets of rarer systems whose collective properties still span the full parameter space of the population, as well as systems containing primary stars that are good age calibrators. Our simulation analysis leads to a series of recommendations for candidate selection and observational follow-up that could identify ˜500 diverse Gaia benchmarks. As a test of the veracity of our methodology and simulations, our initial search uses UKIRT Infrared Deep Sky Survey and Sloan Digital Sky Survey to select secondaries, with the parameters of primaries taken from Tycho-2, Radial Velocity Experiment, Large sky Area Multi-Object fibre Spectroscopic Telescope and Tycho-Gaia Astrometric Solution. We identify and follow up 13 new benchmarks. These include M8-L2 companions, with metallicity constraints ranging in quality, but robust in the range -0.39 ≤ [Fe/H] ≤ +0.36, and with projected physical separation in the range 0.6 < s/kau < 76. Going forward, Gaia offers a very high yield of benchmark systems, from which diverse subsamples may be able to calibrate a range of foundational ultracool/sub-stellar theory and observation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reedlunn, Benjamin

Room D was an in-situ, isothermal, underground experiment conducted at the Waste Isolation Pilot Plant between 1984 and 1991. The room was carefully instrumented to measure the horizontal and vertical closure immediately upon excavation and for several years thereafter. Early finite element simulations of salt creep around Room D under-predicted the vertical closure by 4.5×, causing investigators to explore a series of changes to the way Room D was modeled. Discrepancies between simulations and measurements were resolved through a series of adjustments to model parameters, which were openly acknowledged in published reports. Interest in Room D has been rekindled recentlymore » by the U.S./German Joint Project III and Project WEIMOS, which seek to improve the predictions of rock salt constitutive models. Joint Project participants calibrate their models solely against laboratory tests, and benchmark the models against underground experiments, such as room D. This report describes updating legacy Room D simulations to today’s computational standards by rectifying several numerical issues. Subsequently, the constitutive model used in previous modeling is recalibrated two different ways against a suite of new laboratory creep experiments on salt extracted from the repository horizon of the Waste Isolation Pilot Plant. Simulations with the new, laboratory-based, calibrations under-predict Room D vertical closure by 3.1×. A list of potential improvements is discussed.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reedlunn, Benjamin

Room D was an in-situ, isothermal, underground experiment conducted at theWaste Isolation Pilot Plant between 1984 and 1991. The room was carefully instrumented to measure the horizontal and vertical closure immediately upon excavation and for several years thereafter. Early finite element simulations of salt creep around Room D under predicted the vertical closure by 4.5×, causing investigators to explore a series of changes to the way Room D was modeled. Discrepancies between simulations and measurements were resolved through a series of adjustments to model parameters, which were openly acknowledged in published reports. Interest in Room D has been rekindled recentlymore » by the U.S./German Joint Project III and Project WEIMOS, which seek to improve the predictions of rock salt constitutive models. Joint Project participants calibrate their models solely against laboratory tests, and benchmark the models against underground experiments, such as room D. This report describes updating legacy Room D simulations to today’s computational standards by rectifying several numerical issues. Subsequently, the constitutive model used in previous modeling is recalibrated two different ways against a suite of new laboratory creep experiments on salt extracted from the repository horizon of the Waste Isolation Pilot Plant. Simulations with the new, laboratory-based, calibrations under predict Room D vertical closure by 3.1×. A list of potential improvements is discussed.« less

Modelling of Dispersed Gas-Liquid Flow using LBGK and LPT Approach

NASA Astrophysics Data System (ADS)

Agarwal, Alankar; Prakash, Akshay; Ravindra, B.

2017-11-01

The dynamics of gas bubbles play a significant, if not crucial, role in a large variety of industrial process that involves using reactors. Many of these processes are still not well understood in terms of optimal scale-up strategies.An accurate modeling of bubbles and bubble swarms become important for high fidelity bioreactor simulations. This study is a part of the development of robust bubble fluid interaction modules for simulation of industrial-scale reactors. The work presents the simulation of a single bubble rising in a quiescent water tank using current models presented in the literature for bubble-fluid interaction. In this multiphase benchmark problem, the continuous phase (water) is discretized using the Lattice Bhatnagar-Gross and Krook (LBGK) model of Lattice Boltzmann Method (LBM), while the dispersed gas phase (i.e. air-bubble) modeled with the Lagrangian particle tracking (LPT) approach. The cheap clipped fourth order polynomial function is used to model the interaction between two phases. The model is validated by comparing the simulation results for terminal velocity of a bubble at varying bubble diameter and the influence of bubble motion in liquid velocity with the theoretical and previously available experimental data. This work is supported by the ``Centre for Development of Advanced Computing (C-DAC), Pune'' by providing the advanced computational facility in PARAM Yuva-II.

Evaluation of near surface ozone and particulate matter in air ...

EPA Pesticide Factsheets

In this study, techniques typically used for future air quality projections are applied to a historical 11-year period to assess the performance of the modeling system when the driving meteorological conditions are obtained using dynamical downscaling of coarse-scale fields without correcting toward higher-resolution observations. The Weather Research and Forecasting model and the Community Multiscale Air Quality model are used to simulate regional climate and air quality over the contiguous United States for 2000–2010. The air quality simulations for that historical period are then compared to observations from four national networks. Comparisons are drawn between defined performance metrics and other published modeling results for predicted ozone, fine particulate matter, and speciated fine particulate matter. The results indicate that the historical air quality simulations driven by dynamically downscaled meteorology are typically within defined modeling performance benchmarks and are consistent with results from other published modeling studies using finer-resolution meteorology. This indicates that the regional climate and air quality modeling framework utilized here does not introduce substantial bias, which provides confidence in the method’s use for future air quality projections. This paper shows that if emissions inputs and coarse-scale meteorological inputs are reasonably accurate, then air quality can be simulated with acceptable accuracy even wi

Aeroservoelastic and Flight Dynamics Analysis Using Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Arena, Andrew S., Jr.

1999-01-01

This document in large part is based on the Masters Thesis of Cole Stephens. The document encompasses a variety of technical and practical issues involved when using the STARS codes for Aeroservoelastic analysis of vehicles. The document covers in great detail a number of technical issues and step-by-step details involved in the simulation of a system where aerodynamics, structures and controls are tightly coupled. Comparisons are made to a benchmark experimental program conducted at NASA Langley. One of the significant advantages of the methodology detailed is that as a result of the technique used to accelerate the CFD-based simulation, a systems model is produced which is very useful for developing the control law strategy, and subsequent high-speed simulations.

Testing density-dependent groundwater models: Two-dimensional steady state unstable convection in infinite, finite and inclined porous layers

USGS Publications Warehouse

Weatherill, D.; Simmons, C.T.; Voss, C.I.; Robinson, N.I.

2004-01-01

This study proposes the use of several problems of unstable steady state convection with variable fluid density in a porous layer of infinite horizontal extent as two-dimensional (2-D) test cases for density-dependent groundwater flow and solute transport simulators. Unlike existing density-dependent model benchmarks, these problems have well-defined stability criteria that are determined analytically. These analytical stability indicators can be compared with numerical model results to test the ability of a code to accurately simulate buoyancy driven flow and diffusion. The basic analytical solution is for a horizontally infinite fluid-filled porous layer in which fluid density decreases with depth. The proposed test problems include unstable convection in an infinite horizontal box, in a finite horizontal box, and in an infinite inclined box. A dimensionless Rayleigh number incorporating properties of the fluid and the porous media determines the stability of the layer in each case. Testing the ability of numerical codes to match both the critical Rayleigh number at which convection occurs and the wavelength of convection cells is an addition to the benchmark problems currently in use. The proposed test problems are modelled in 2-D using the SUTRA [SUTRA-A model for saturated-unsaturated variable-density ground-water flow with solute or energy transport. US Geological Survey Water-Resources Investigations Report, 02-4231, 2002. 250 p] density-dependent groundwater flow and solute transport code. For the case of an infinite horizontal box, SUTRA results show a distinct change from stable to unstable behaviour around the theoretical critical Rayleigh number of 4??2 and the simulated wavelength of unstable convection agrees with that predicted by the analytical solution. The effects of finite layer aspect ratio and inclination on stability indicators are also tested and numerical results are in excellent agreement with theoretical stability criteria and with numerical results previously reported in traditional fluid mechanics literature. ?? 2004 Elsevier Ltd. All rights reserved.

Seltzer_et_al_2016

EPA Pesticide Factsheets

This dataset supports the modeling study of Seltzer et al. (2016) published in Atmospheric Environment. In this study, techniques typically used for future air quality projections are applied to a historical 11-year period to assess the performance of the modeling system when the driving meteorological conditions are obtained using dynamical downscaling of coarse-scale fields without correcting toward higher resolution observations. The Weather Research and Forecasting model and the Community Multiscale Air Quality model are used to simulate regional climate and air quality over the contiguous United States for 2000-2010. The air quality simulations for that historical period are then compared to observations from four national networks. Comparisons are drawn between defined performance metrics and other published modeling results for predicted ozone, fine particulate matter, and speciated fine particulate matter. The results indicate that the historical air quality simulations driven by dynamically downscaled meteorology are typically within defined modeling performance benchmarks and are consistent with results from other published modeling studies using finer-resolution meteorology. This indicates that the regional climate and air quality modeling framework utilized here does not introduce substantial bias, which provides confidence in the method??s use for future air quality projections.This dataset is associated with the following publication:Seltzer, K., C

Mesoscale Modeling of LX-17 Under Isentropic Compression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Springer, H K; Willey, T M; Friedman, G

Mesoscale simulations of LX-17 incorporating different equilibrium mixture models were used to investigate the unreacted equation-of-state (UEOS) of TATB. Candidate TATB UEOS were calculated using the equilibrium mixture models and benchmarked with mesoscale simulations of isentropic compression experiments (ICE). X-ray computed tomography (XRCT) data provided the basis for initializing the simulations with realistic microstructural details. Three equilibrium mixture models were used in this study. The single constituent with conservation equations (SCCE) model was based on a mass-fraction weighted specific volume and the conservation of mass, momentum, and energy. The single constituent equation-of-state (SCEOS) model was based on a mass-fraction weightedmore » specific volume and the equation-of-state of the constituents. The kinetic energy averaging (KEA) model was based on a mass-fraction weighted particle velocity mixture rule and the conservation equations. The SCEOS model yielded the stiffest TATB EOS (0.121{micro} + 0.4958{micro}{sup 2} + 2.0473{micro}{sup 3}) and, when incorporated in mesoscale simulations of the ICE, demonstrated the best agreement with VISAR velocity data for both specimen thicknesses. The SCCE model yielded a relatively more compliant EOS (0.1999{micro}-0.6967{micro}{sup 2} + 4.9546{micro}{sup 3}) and the KEA model yielded the most compliant EOS (0.1999{micro}-0.6967{micro}{sup 2}+4.9546{micro}{sup 3}) of all the equilibrium mixture models. Mesoscale simulations with the lower density TATB adiabatic EOS data demonstrated the least agreement with VISAR velocity data.« less

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

PubMed

Marquez-Lago, Tatiana T; Burrage, Kevin

2007-09-14

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.

Benchmarking of software tools for optical proximity correction

NASA Astrophysics Data System (ADS)

Jungmann, Angelika; Thiele, Joerg; Friedrich, Christoph M.; Pforr, Rainer; Maurer, Wilhelm

1998-06-01

The point when optical proximity correction (OPC) will become a routine procedure for every design is not far away. For such a daily use the requirements for an OPC tool go far beyond the principal functionality of OPC that was proven by a number of approaches and is documented well in literature. In this paper we first discuss the requirements for a productive OPC tool. Against these requirements a benchmarking was performed with three different OPC tools available on market (OPRX from TVT, OPTISSIMO from aiss and PROTEUS from TMA). Each of these tools uses a different approach to perform the correction (rules, simulation or model). To assess the accuracy of the correction, a test chip was fabricated, which contains corrections done by each software tool. The advantages and weakness of the several solutions are discussed.

The philosophy of benchmark testing a standards-based picture archiving and communications system.

PubMed

Richardson, N E; Thomas, J A; Lyche, D K; Romlein, J; Norton, G S; Dolecek, Q E

1999-05-01

The Department of Defense issued its requirements for a Digital Imaging Network-Picture Archiving and Communications System (DIN-PACS) in a Request for Proposals (RFP) to industry in January 1997, with subsequent contracts being awarded in November 1997 to the Agfa Division of Bayer and IBM Global Government Industry. The Government's technical evaluation process consisted of evaluating a written technical proposal as well as conducting a benchmark test of each proposed system at the vendor's test facility. The purpose of benchmark testing was to evaluate the performance of the fully integrated system in a simulated operational environment. The benchmark test procedures and test equipment were developed through a joint effort between the Government, academic institutions, and private consultants. Herein the authors discuss the resources required and the methods used to benchmark test a standards-based PACS.

Benchmarking NWP Kernels on Multi- and Many-core Processors

NASA Astrophysics Data System (ADS)

Michalakes, J.; Vachharajani, M.

2008-12-01

Increased computing power for weather, climate, and atmospheric science has provided direct benefits for defense, agriculture, the economy, the environment, and public welfare and convenience. Today, very large clusters with many thousands of processors are allowing scientists to move forward with simulations of unprecedented size. But time-critical applications such as real-time forecasting or climate prediction need strong scaling: faster nodes and processors, not more of them. Moreover, the need for good cost- performance has never been greater, both in terms of performance per watt and per dollar. For these reasons, the new generations of multi- and many-core processors being mass produced for commercial IT and "graphical computing" (video games) are being scrutinized for their ability to exploit the abundant fine- grain parallelism in atmospheric models. We present results of our work to date identifying key computational kernels within the dynamics and physics of a large community NWP model, the Weather Research and Forecast (WRF) model. We benchmark and optimize these kernels on several different multi- and many-core processors. The goals are to (1) characterize and model performance of the kernels in terms of computational intensity, data parallelism, memory bandwidth pressure, memory footprint, etc. (2) enumerate and classify effective strategies for coding and optimizing for these new processors, (3) assess difficulties and opportunities for tool or higher-level language support, and (4) establish a continuing set of kernel benchmarks that can be used to measure and compare effectiveness of current and future designs of multi- and many-core processors for weather and climate applications.

Performance of MODIS satellite and mesoscale model based land surface temperature for soil moisture deficit estimation using Neural Network

NASA Astrophysics Data System (ADS)

Srivastava, Prashant K.; Petropoulos, George P.; Gupta, Manika; Islam, Tanvir

2015-04-01

Soil Moisture Deficit (SMD) is a key variable in the water and energy exchanges that occur at the land-surface/atmosphere interface. Monitoring SMD is an alternate method of irrigation scheduling and represents the use of the suitable quantity of water at the proper time by combining measurements of soil moisture deficit. In past it is found that LST has a strong relation to SMD, which can be estimated by MODIS or numerical weather prediction model such as WRF (Weather Research and Forecasting model). By looking into the importance of SMD, this work focused on the application of Artificial Neural Network (ANN) for evaluating its capabilities towards SMD estimation using the LST data estimated from MODIS and WRF mesoscale model. The benchmark SMD estimated from Probability Distribution Model (PDM) over the Brue catchment, Southwest of England, U.K. is used for all the calibration and validation experiments. The performances between observed and simulated SMD are assessed in terms of the Nash-Sutcliffe Efficiency (NSE), the Root Mean Square Error (RMSE) and the percentage of bias (%Bias). The application of the ANN confirmed a high capability WRF and MODIS LST for prediction of SMD. Performance during the ANN calibration and validation showed a good agreement between benchmark and estimated SMD with MODIS LST information with significantly higher performance than WRF simulated LST. The work presented showed the first comprehensive application of LST from MODIS and WRF mesoscale model for hydrological SMD estimation, particularly for the maritime climate. More studies in this direction are recommended to hydro-meteorological community, so that useful information will be accumulated in the technical literature domain for different geographical locations and climatic conditions. Keyword: WRF, Land Surface Temperature, MODIS satellite, Soil Moisture Deficit, Neural Network

Thermal-chemical Mantle Convection Models With Adaptive Mesh Refinement

NASA Astrophysics Data System (ADS)

Leng, W.; Zhong, S.

2008-12-01

In numerical modeling of mantle convection, resolution is often crucial for resolving small-scale features. New techniques, adaptive mesh refinement (AMR), allow local mesh refinement wherever high resolution is needed, while leaving other regions with relatively low resolution. Both computational efficiency for large- scale simulation and accuracy for small-scale features can thus be achieved with AMR. Based on the octree data structure [Tu et al. 2005], we implement the AMR techniques into the 2-D mantle convection models. For pure thermal convection models, benchmark tests show that our code can achieve high accuracy with relatively small number of elements both for isoviscous cases (i.e. 7492 AMR elements v.s. 65536 uniform elements) and for temperature-dependent viscosity cases (i.e. 14620 AMR elements v.s. 65536 uniform elements). We further implement tracer-method into the models for simulating thermal-chemical convection. By appropriately adding and removing tracers according to the refinement of the meshes, our code successfully reproduces the benchmark results in van Keken et al. [1997] with much fewer elements and tracers compared with uniform-mesh models (i.e. 7552 AMR elements v.s. 16384 uniform elements, and ~83000 tracers v.s. ~410000 tracers). The boundaries of the chemical piles in our AMR code can be easily refined to the scales of a few kilometers for the Earth's mantle and the tracers are concentrated near the chemical boundaries to precisely trace the evolvement of the boundaries. It is thus very suitable for our AMR code to study the thermal-chemical convection problems which need high resolution to resolve the evolvement of chemical boundaries, such as the entrainment problems [Sleep, 1988].

Fast quantum Monte Carlo on a GPU

NASA Astrophysics Data System (ADS)

Lutsyshyn, Y.

2015-02-01

We present a scheme for the parallelization of quantum Monte Carlo method on graphical processing units, focusing on variational Monte Carlo simulation of bosonic systems. We use asynchronous execution schemes with shared memory persistence, and obtain an excellent utilization of the accelerator. The CUDA code is provided along with a package that simulates liquid helium-4. The program was benchmarked on several models of Nvidia GPU, including Fermi GTX560 and M2090, and the Kepler architecture K20 GPU. Special optimization was developed for the Kepler cards, including placement of data structures in the register space of the Kepler GPUs. Kepler-specific optimization is discussed.

Half-Cell RF Gun Simulations with the Electromagnetic Particle-in-Cell Code VORPAL

NASA Astrophysics Data System (ADS)

Paul, K.; Dimitrov, D. A.; Busby, R.; Bruhwiler, D. L.; Smithe, D.; Cary, J. R.; Kewisch, J.; Kayran, D.; Calaga, R.; Ben-Zvi, I.

2009-01-01

We have simulated Brookhaven National Laboratory's half-cell superconducting RF gun design for a proposed high-current ERL using the three-dimensional, electromagnetic particle-in-cell code VORPAL. VORPAL computes the fully self-consistent electromagnetic fields produced by the electron bunches, meaning that it accurately models space-charge effects as well as bunch-to-bunch beam loading effects and the effects of higher-order cavity modes, though these are beyond the scope of this paper. We compare results from VORPAL to the well-established space-charge code PARMELA, using RF fields produced by SUPERFISH, as a benchmarking exercise in which the two codes should agree well.

Evolvable mathematical models: A new artificial Intelligence paradigm

NASA Astrophysics Data System (ADS)

Grouchy, Paul

We develop a novel Artificial Intelligence paradigm to generate autonomously artificial agents as mathematical models of behaviour. Agent/environment inputs are mapped to agent outputs via equation trees which are evolved in a manner similar to Symbolic Regression in Genetic Programming. Equations are comprised of only the four basic mathematical operators, addition, subtraction, multiplication and division, as well as input and output variables and constants. From these operations, equations can be constructed that approximate any analytic function. These Evolvable Mathematical Models (EMMs) are tested and compared to their Artificial Neural Network (ANN) counterparts on two benchmarking tasks: the double-pole balancing without velocity information benchmark and the challenging discrete Double-T Maze experiments with homing. The results from these experiments show that EMMs are capable of solving tasks typically solved by ANNs, and that they have the ability to produce agents that demonstrate learning behaviours. To further explore the capabilities of EMMs, as well as to investigate the evolutionary origins of communication, we develop NoiseWorld, an Artificial Life simulation in which interagent communication emerges and evolves from initially noncommunicating EMM-based agents. Agents develop the capability to transmit their x and y position information over a one-dimensional channel via a complex, dialogue-based communication scheme. These evolved communication schemes are analyzed and their evolutionary trajectories examined, yielding significant insight into the emergence and subsequent evolution of cooperative communication. Evolved agents from NoiseWorld are successfully transferred onto physical robots, demonstrating the transferability of EMM-based AIs from simulation into physical reality.

Constraints on long-term carbon-climate feedbacks from spatially resolved CO2 growth rate fluctuations linked to temperature and precipitation

NASA Astrophysics Data System (ADS)

Keppel-Aleks, G.; Hoffman, F. M.

2014-12-01

Feedbacks between the global carbon cycle and climate represent one of the largest uncertainties in climate prediction. A promising method for reducing uncertainty in predictions of carbon-climate feedbacks is based on identifying an "emergent constraint" that leverages correlations between mechanistically linked long-term feedbacks and short-term variations within the model ensemble. By applying contemporary observations to evaluate model skill in simulating short-term variations, we may be able to better assess the probability of simulated long-term feedbacks. We probed the constraint on long-term terrestrial carbon stocks provided by climate-driven fluctuations in the atmospheric CO2 growth rate at contemporary timescales. We considered the impact of both temperature and precipitation anomalies on terrestrial ecosystem exchange and further separated the direct influence of fire where possible. When we explicitly considered the role of atmospheric transport in smoothing the imprint of climate-driven flux anomalies on atmospheric CO2 patterns, we found that the extent of temporal averaging of both the observations and ESM output leads to estimates for the long-term climate sensitivity of tropical land carbon storage that are different by a factor of two. In the context of these results, we discuss strategies for applying emergent constraints for benchmarking biogeochemical feedbacks in ESMs. Specifically, our results underscore the importance of selecting appropriate observational benchmarks and, for future model intercomparison projects, outputting fields that most closely correspond to available observational datasets.

Technical Report: Benchmarking for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLoughlin, K.

2016-01-22

The software application “MetaQuant” was developed by our group at Lawrence Livermore National Laboratory (LLNL). It is designed to profile microbial populations in a sample using data from whole-genome shotgun (WGS) metagenomic DNA sequencing. Several other metagenomic profiling applications have been described in the literature. We ran a series of benchmark tests to compare the performance of MetaQuant against that of a few existing profiling tools, using real and simulated sequence datasets. This report describes our benchmarking procedure and results.

History matching through dynamic decision-making

PubMed Central

Maschio, Célio; Santos, Antonio Alberto; Schiozer, Denis; Rocha, Anderson

2017-01-01

History matching is the process of modifying the uncertain attributes of a reservoir model to reproduce the real reservoir performance. It is a classical reservoir engineering problem and plays an important role in reservoir management since the resulting models are used to support decisions in other tasks such as economic analysis and production strategy. This work introduces a dynamic decision-making optimization framework for history matching problems in which new models are generated based on, and guided by, the dynamic analysis of the data of available solutions. The optimization framework follows a ‘learning-from-data’ approach, and includes two optimizer components that use machine learning techniques, such as unsupervised learning and statistical analysis, to uncover patterns of input attributes that lead to good output responses. These patterns are used to support the decision-making process while generating new, and better, history matched solutions. The proposed framework is applied to a benchmark model (UNISIM-I-H) based on the Namorado field in Brazil. Results show the potential the dynamic decision-making optimization framework has for improving the quality of history matching solutions using a substantial smaller number of simulations when compared with a previous work on the same benchmark. PMID:28582413

Benchmarking carbon-nitrogen interactions in Earth System Models to observations: An inter-comparison of nitrogen limitation in global land surface models with carbon and nitrogen cycles (CLM-CN and O-CN)

NASA Astrophysics Data System (ADS)

Thomas, R. Q.; Zaehle, S.; Templer, P. H.; Goodale, C. L.

2011-12-01

Predictions of climate change depend on accurately modeling the feedbacks among the carbon cycle, nitrogen cycle, and climate system. Several global land surface models have shown that nitrogen limitation determines how land carbon fluxes respond to rising CO2, nitrogen deposition, and climate change, thereby influencing predictions of climate change. However, the magnitude of the carbon-nitrogen-climate feedbacks varies considerably by model, leading to critical and timely questions of why they differ and how they compare to field observations. To address these questions, we initiated a model inter-comparison of spatial patterns and drivers of nitrogen limitation. The experiment assessed the regional consequences of sustained nitrogen additions in a set of 25-year global nitrogen fertilization simulations. The model experiments were designed to cover effects from small changes in nitrogen inputs associated with plausible increases in nitrogen deposition to large changes associated with field-based nitrogen fertilization experiments. The analyses of model simulations included assessing the geographically varying degree of nitrogen limitation on plant and soil carbon cycling and the mechanisms underlying model differences. Here, we present results from two global land-surface models (CLM-CN and O-CN) with differing approaches to modeling carbon-nitrogen interactions. The predictions from each model were compared to a set of globally distributed observational data that includes nitrogen fertilization experiments, 15N tracer studies, small catchment nitrogen input-output studies, and syntheses across nitrogen deposition gradients. Together these datasets test many aspects of carbon-nitrogen coupling and are able to differentiate between the two models. Overall, this study is the first to explicitly benchmark carbon and nitrogen interactions in Earth System Models using a range of observations and is a foundation for future inter-comparisons.

Towards modelling of water inflow into the mantle

NASA Astrophysics Data System (ADS)

Thielmann, M.; Eichheimer, P.; Golabek, G.

2017-12-01

The transport and storage of water in the mantle significantly affects various material properties of mantle rocks and thus water plays a key role in a variety of geodynamical processes (tectonics, magmatism etc.) Geological and seismological observations suggest different inflow mechanisms of water via the subducting slab like slab bending, thermal cracking and serpentinization (Faccenda et al., 2009; Korenaga, 2017). Most of the previous numerical models do not take different dip angles of the subduction slab and subduction velocities into account, while nature provides two different types of subduction regimes i.e. shallow and deep subduction (Li et al., 2011). To which extent both parameters influence the inflow and outflow of water in the mantle still remains unclear. For the investigation of the inflow and outflow of fluids e.g. water in the mantle, we use high resolution 2D finite element simulations, which allow us to resolve subducted sediments and crustal layers. For this purpose the finite element code MVEP2 (Kaus, 2010), is tested against benchmark results (van Keken et al., 2008). In a first step we reproduced the analytical cornerflow model (Batchelor, 1967) used in the benchmark of van Keken et al.(2008) as well as the steady state temperature field. Further steps consist of successively increasing model complexity, such as the incorporation of hydrogen diffusion, water transport and dehydration reactions. ReferencesBatchelor, G. K. An Introduction to Fluid Dynamics. Cambridge University Press, Cambridge, UK (1967) van Keken, P. E., et al. A community benchmark for subduction zone modeling. Phys. Earth Planet. Int. 171, 187-197 (2008). Faccenda, M., T.V. Gerya, and L. Burlini. Deep slab hydration induced by bending-related variations in tectonic pressure. Nat. Geosci. 2, 790-793 (2009). Korenaga, J. On the extent of mantle hydration caused by plate bending. Earth Planet. Sci. Lett. 457, 1-9 (2017). Li, Z. H., Xu, Z. Q., and T.V. Gerya. Flat versus steep subduction: Contrasting modes for the formation and exhumation of high- to ultrahigh-pressure rocks in continental collision zones. Earth Planet. Sci. Lett. 301, 65-77 (2011). Kaus, B. J. P. Factors that control the angle of shear bands in geodynamic numerical models of brittle deformation. Tectonophys. 484, 36-47 (2010). The transport and storage of water in the mantle significantly affects various material properties of mantle rocks and thus water plays a key role in a variety of geodynamical processes (tectonics, magmatism etc.) Geological and seismological observations suggest different inflow mechanisms of water via the subducting slab like slab bending, thermal cracking and serpentinization (Faccenda et al., 2009; Korenaga, 2017). Most of the previous numerical models do not take different dip angles of the subduction slab and subduction velocities into account, while nature provides two different types of subduction regimes i.e. shallow and deep subduction (Li et al., 2011). To which extent both parameters influence the inflow and outflow of water in the mantle still remains unclear. For the investigation of the inflow and outflow of fluids e.g. water in the mantle, we use high resolution 2D finite element simulations, which allow us to resolve subducted sediments and crustal layers. For this purpose the finite element code MVEP2 (Kaus, 2010), is tested against benchmark results (van Keken et al., 2008). In a first step we reproduced the analytical cornerflow model (Batchelor, 1967) used in the benchmark of van Keken et al.(2008) as well as the steady state temperature field.Further steps consist of successively increasing model complexity, such as the incorporation of hydrogen diffusion, water transport and dehydration reactions. Systematic simulations are performed to assess the influence of different model parameters on various target parameters such as dehydration depth, volcanic line position etc., the ultimate goal being the derivation of scaling laws for water transport in the mantleReferencesBatchelor, G. K. An Introduction to Fluid Dynamics. Cambridge University Press, Cambridge, UK (1967)van Keken, P. E., et al. A community benchmark for subduction zone modeling. Phys. Earth Planet. Int. 171, 187-197 (2008). Faccenda, M., T.V. Gerya, and L. Burlini. Deep slab hydration induced by bending-related variations in tectonic pressure. Nat. Geosci. 2, 790-793 (2009). Korenaga, J. On the extent of mantle hydration caused by plate bending. Earth Planet. Sci. Lett. 457, 1-9 (2017). Li, Z. H., Xu, Z. Q., and T.V. Gerya. Flat versus steep subduction: Contrasting modes for the formation and exhumation of high- to ultrahigh-pressure rocks in continental collision zones. Earth Planet. Sci. Lett. 301, 65-77 (2011). Kaus, B. J. P. Factors that control the angle of shear bands in geodynamic numerical models of brittle deformation. Tectonophys. 484, 36-47 (2010).

EPA and EFSA approaches for Benchmark Dose modeling

EPA Science Inventory

Benchmark dose (BMD) modeling has become the preferred approach in the analysis of toxicological dose-response data for the purpose of deriving human health toxicity values. The software packages most often used are Benchmark Dose Software (BMDS, developed by EPA) and PROAST (de...

Realistic simulations of a cyclotron spiral inflector within a particle-in-cell framework

NASA Astrophysics Data System (ADS)

Winklehner, Daniel; Adelmann, Andreas; Gsell, Achim; Kaman, Tulin; Campo, Daniela

2017-12-01

We present an upgrade to the particle-in-cell ion beam simulation code opal that enables us to run highly realistic simulations of the spiral inflector system of a compact cyclotron. This upgrade includes a new geometry class and field solver that can handle the complicated boundary conditions posed by the electrode system in the central region of the cyclotron both in terms of particle termination, and calculation of self-fields. Results are benchmarked against the analytical solution of a coasting beam. As a practical example, the spiral inflector and the first revolution in a 1 MeV /amu test cyclotron, located at Best Cyclotron Systems, Inc., are modeled and compared to the simulation results. We find that opal can now handle arbitrary boundary geometries with relative ease. Simulated injection efficiencies and beam shape compare well with measured efficiencies and a preliminary measurement of the beam distribution after injection.

Extension of PENELOPE to protons: simulation of nuclear reactions and benchmark with Geant4.

PubMed

Sterpin, E; Sorriaux, J; Vynckier, S

2013-11-01

Describing the implementation of nuclear reactions in the extension of the Monte Carlo code (MC) PENELOPE to protons (PENH) and benchmarking with Geant4. PENH is based on mixed-simulation mechanics for both elastic and inelastic electromagnetic collisions (EM). The adopted differential cross sections for EM elastic collisions are calculated using the eikonal approximation with the Dirac-Hartree-Fock-Slater atomic potential. Cross sections for EM inelastic collisions are computed within the relativistic Born approximation, using the Sternheimer-Liljequist model of the generalized oscillator strength. Nuclear elastic and inelastic collisions were simulated using explicitly the scattering analysis interactive dialin database for (1)H and ICRU 63 data for (12)C, (14)N, (16)O, (31)P, and (40)Ca. Secondary protons, alphas, and deuterons were all simulated as protons, with the energy adapted to ensure consistent range. Prompt gamma emission can also be simulated upon user request. Simulations were performed in a water phantom with nuclear interactions switched off or on and integral depth-dose distributions were compared. Binary-cascade and precompound models were used for Geant4. Initial energies of 100 and 250 MeV were considered. For cases with no nuclear interactions simulated, additional simulations in a water phantom with tight resolution (1 mm in all directions) were performed with FLUKA. Finally, integral depth-dose distributions for a 250 MeV energy were computed with Geant4 and PENH in a homogeneous phantom with, first, ICRU striated muscle and, second, ICRU compact bone. For simulations with EM collisions only, integral depth-dose distributions were within 1%/1 mm for doses higher than 10% of the Bragg-peak dose. For central-axis depth-dose and lateral profiles in a phantom with tight resolution, there are significant deviations between Geant4 and PENH (up to 60%/1 cm for depth-dose distributions). The agreement is much better with FLUKA, with deviations within 3%/3 mm. When nuclear interactions were turned on, agreement (within 6% before the Bragg-peak) between PENH and Geant4 was consistent with uncertainties on nuclear models and cross sections, whatever the material simulated (water, muscle, or bone). A detailed and flexible description of nuclear reactions has been implemented in the PENH extension of PENELOPE to protons, which utilizes a mixed-simulation scheme for both elastic and inelastic EM collisions, analogous to the well-established algorithm for electrons/positrons. PENH is compatible with all current main programs that use PENELOPE as the MC engine. The nuclear model of PENH is realistic enough to give dose distributions in fair agreement with those computed by Geant4.

Extension of PENELOPE to protons: Simulation of nuclear reactions and benchmark with Geant4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sterpin, E.; Sorriaux, J.; Vynckier, S.

2013-11-15

Purpose: Describing the implementation of nuclear reactions in the extension of the Monte Carlo code (MC) PENELOPE to protons (PENH) and benchmarking with Geant4.Methods: PENH is based on mixed-simulation mechanics for both elastic and inelastic electromagnetic collisions (EM). The adopted differential cross sections for EM elastic collisions are calculated using the eikonal approximation with the Dirac–Hartree–Fock–Slater atomic potential. Cross sections for EM inelastic collisions are computed within the relativistic Born approximation, using the Sternheimer–Liljequist model of the generalized oscillator strength. Nuclear elastic and inelastic collisions were simulated using explicitly the scattering analysis interactive dialin database for {sup 1}H and ICRUmore » 63 data for {sup 12}C, {sup 14}N, {sup 16}O, {sup 31}P, and {sup 40}Ca. Secondary protons, alphas, and deuterons were all simulated as protons, with the energy adapted to ensure consistent range. Prompt gamma emission can also be simulated upon user request. Simulations were performed in a water phantom with nuclear interactions switched off or on and integral depth–dose distributions were compared. Binary-cascade and precompound models were used for Geant4. Initial energies of 100 and 250 MeV were considered. For cases with no nuclear interactions simulated, additional simulations in a water phantom with tight resolution (1 mm in all directions) were performed with FLUKA. Finally, integral depth–dose distributions for a 250 MeV energy were computed with Geant4 and PENH in a homogeneous phantom with, first, ICRU striated muscle and, second, ICRU compact bone.Results: For simulations with EM collisions only, integral depth–dose distributions were within 1%/1 mm for doses higher than 10% of the Bragg-peak dose. For central-axis depth–dose and lateral profiles in a phantom with tight resolution, there are significant deviations between Geant4 and PENH (up to 60%/1 cm for depth–dose distributions). The agreement is much better with FLUKA, with deviations within 3%/3 mm. When nuclear interactions were turned on, agreement (within 6% before the Bragg-peak) between PENH and Geant4 was consistent with uncertainties on nuclear models and cross sections, whatever the material simulated (water, muscle, or bone).Conclusions: A detailed and flexible description of nuclear reactions has been implemented in the PENH extension of PENELOPE to protons, which utilizes a mixed-simulation scheme for both elastic and inelastic EM collisions, analogous to the well-established algorithm for electrons/positrons. PENH is compatible with all current main programs that use PENELOPE as the MC engine. The nuclear model of PENH is realistic enough to give dose distributions in fair agreement with those computed by Geant4.« less

Modelling solute dispersion in periodic heterogeneous porous media: Model benchmarking against intermediate scale experiments

NASA Astrophysics Data System (ADS)

Majdalani, Samer; Guinot, Vincent; Delenne, Carole; Gebran, Hicham

2018-06-01

This paper is devoted to theoretical and experimental investigations of solute dispersion in heterogeneous porous media. Dispersion in heterogenous porous media has been reported to be scale-dependent, a likely indication that the proposed dispersion models are incompletely formulated. A high quality experimental data set of breakthrough curves in periodic model heterogeneous porous media is presented. In contrast with most previously published experiments, the present experiments involve numerous replicates. This allows the statistical variability of experimental data to be accounted for. Several models are benchmarked against the data set: the Fickian-based advection-dispersion, mobile-immobile, multirate, multiple region advection dispersion models, and a newly proposed transport model based on pure advection. A salient property of the latter model is that its solutions exhibit a ballistic behaviour for small times, while tending to the Fickian behaviour for large time scales. Model performance is assessed using a novel objective function accounting for the statistical variability of the experimental data set, while putting equal emphasis on both small and large time scale behaviours. Besides being as accurate as the other models, the new purely advective model has the advantages that (i) it does not exhibit the undesirable effects associated with the usual Fickian operator (namely the infinite solute front propagation speed), and (ii) it allows dispersive transport to be simulated on every heterogeneity scale using scale-independent parameters.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium.

PubMed

Han, Jeong-Hwan; Oda, Takuji

2018-04-14

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium

NASA Astrophysics Data System (ADS)

Han, Jeong-Hwan; Oda, Takuji

2018-04-01

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

An Integrated Development Environment for Adiabatic Quantum Programming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humble, Travis S; McCaskey, Alex; Bennink, Ryan S

2014-01-01

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware raises the question of how well quantum programs perform. Benchmarking behavior is challenging since the multiple steps to synthesize an adiabatic quantum program are highly tunable. We present an adiabatic quantum programming environment called JADE that provides control over all the steps taken during program development. JADE captures the workflow needed to rigorously benchmark performance while also allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation enginemore » that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its use for benchmarking adiabatic quantum programs.« less

Wall Modeled Large Eddy Simulation of Airfoil Trailing Edge Noise

NASA Astrophysics Data System (ADS)

Kocheemoolayil, Joseph; Lele, Sanjiva

2014-11-01

Large eddy simulation (LES) of airfoil trailing edge noise has largely been restricted to low Reynolds numbers due to prohibitive computational cost. Wall modeled LES (WMLES) is a computationally cheaper alternative that makes full-scale Reynolds numbers relevant to large wind turbines accessible. A systematic investigation of trailing edge noise prediction using WMLES is conducted. Detailed comparisons are made with experimental data. The stress boundary condition from a wall model does not constrain the fluctuating velocity to vanish at the wall. This limitation has profound implications for trailing edge noise prediction. The simulation over-predicts the intensity of fluctuating wall pressure and far-field noise. An improved wall model formulation that minimizes the over-prediction of fluctuating wall pressure is proposed and carefully validated. The flow configurations chosen for the study are from the workshop on benchmark problems for airframe noise computations. The large eddy simulation database is used to examine the adequacy of scaling laws that quantify the dependence of trailing edge noise on Mach number, Reynolds number and angle of attack. Simplifying assumptions invoked in engineering approaches towards predicting trailing edge noise are critically evaluated. We gratefully acknowledge financial support from GE Global Research and thank Cascade Technologies Inc. for providing access to their massively-parallel large eddy simulation framework.

Resolved-particle simulation by the Physalis method: Enhancements and new capabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sierakowski, Adam J., E-mail: sierakowski@jhu.edu; Prosperetti, Andrea; Faculty of Science and Technology and J.M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede

2016-03-15

We present enhancements and new capabilities of the Physalis method for simulating disperse multiphase flows using particle-resolved simulation. The current work enhances the previous method by incorporating a new type of pressure-Poisson solver that couples with a new Physalis particle pressure boundary condition scheme and a new particle interior treatment to significantly improve overall numerical efficiency. Further, we implement a more efficient method of calculating the Physalis scalar products and incorporate short-range particle interaction models. We provide validation and benchmarking for the Physalis method against experiments of a sedimenting particle and of normal wall collisions. We conclude with an illustrativemore » simulation of 2048 particles sedimenting in a duct. In the appendix, we present a complete and self-consistent description of the analytical development and numerical methods.« less

Simulation of wake effects between two wind farms

NASA Astrophysics Data System (ADS)

Hansen, K. S.; Réthoré, P.-E.; Palma, J.; Hevia, B. G.; Prospathopoulos, J.; Peña, A.; Ott, S.; Schepers, G.; Palomares, A.; van der Laan, M. P.; Volker, P.

2015-06-01

SCADA data, recorded on the downstream wind farm, has been used to identify flow cases with visible clustering effects. The inflow condition is derived from a partly undisturbed wind turbine, due to lack of mast measurements. The SCADA data analysis concludes that centre of the deficit for the downstream wind farm with disturbed inflow has a distinct visible maximum deficit zone located only 5-10D downstream from the entrance. This zone, representing 20-30% speed reduction, increases and moves downstream for increasing cluster effect and is not visible outside a flow sector of 20-30°. The eight flow models represented in this benchmark include both RANS models, mesoscale models and engineering models. The flow cases, identified according to the wind speed level and inflow sector, have been simulated and validated with the SCADA results. The model validation concludes that all models more or less are able to predict the location and size of the deficit zone inside the downwind wind farm.

The PPP Simulator: User’s Manual and Report

DTIC Science & Technology

1986-11-01

simulator: Script started on Thu Aug 28 09:16:15 1986 1 ji] -> ppp -d Benchmarks/Par/ccon6.w pau load /a/hprg’fagin/ PPPl /Benchmarks/Par,’concatOP .w Capace...EOF ) putc( c, stdout ) #else if(( fp = fopen("/a/hprg/fagin/ PPPl /notes’, fir" ))!NULL) while(( c = getc(fp)) != EOF ) putc( c, stdout ) #erndif if...hprg/fagin/ PPPl /bitl.d’, fir" ) =NULL) lddsptbl( fp, bi-tbl ); while((--argc > 0) && ((*.+argv)[0]= -I for( s =argv[0]+l; *s!=’\\0’ s++ A -A Aug 18 16

Summary of the Tandem Cylinder Solutions from the Benchmark Problems for Airframe Noise Computations-I Workshop

NASA Technical Reports Server (NTRS)

Lockard, David P.

2011-01-01

Fifteen submissions in the tandem cylinders category of the First Workshop on Benchmark problems for Airframe Noise Computations are summarized. Although the geometry is relatively simple, the problem involves complex physics. Researchers employed various block-structured, overset, unstructured and embedded Cartesian grid techniques and considerable computational resources to simulate the flow. The solutions are compared against each other and experimental data from 2 facilities. Overall, the simulations captured the gross features of the flow, but resolving all the details which would be necessary to compute the noise remains challenging. In particular, how to best simulate the effects of the experimental transition strip, and the associated high Reynolds number effects, was unclear. Furthermore, capturing the spanwise variation proved difficult.

Policy choices in dementia care-An exploratory analysis of the Alberta continuing care system (ACCS) using system dynamics.

PubMed

Cepoiu-Martin, Monica; Bischak, Diane P

2018-02-01

The increase in the incidence of dementia in the aging population and the decrease in the availability of informal caregivers put pressure on continuing care systems to care for a growing number of people with disabilities. Policy changes in the continuing care system need to address this shift in the population structure. One of the most effective tools for assessing policies in complex systems is system dynamics. Nevertheless, this method is underused in continuing care capacity planning. A system dynamics model of the Alberta Continuing Care System was developed using stylized data. Sensitivity analyses and policy evaluations were conducted to demonstrate the use of system dynamics modelling in this area of public health planning. We focused our policy exploration on introducing staff/resident benchmarks in both supportive living and long-term care (LTC). The sensitivity analyses presented in this paper help identify leverage points in the system that need to be acknowledged when policy decisions are made. Our policy explorations showed that the deficits of staff increase dramatically when benchmarks are introduced, as expected, but at the end of the simulation period, the difference in deficits of both nurses and health care aids are similar between the 2 scenarios tested. Modifying the benchmarks in LTC only versus in both supportive living and LTC has similar effects on staff deficits in long term, under the assumptions of this particular model. The continuing care system dynamics model can be used to test various policy scenarios, allowing decision makers to visualize the effect of a certain policy choice on different system variables and to compare different policy options. Our exploration illustrates the use of system dynamics models for policy making in complex health care systems. © 2017 John Wiley & Sons, Ltd.

Simulations of Seismic Wave Propagation on Mars

DOE PAGES

Bozdağ, Ebru; Ruan, Youyi; Metthez, Nathan; ...

2017-03-23

In this paper, we present global and regional synthetic seismograms computed for 1D and 3D Mars models based on the spectral-element method. For global simulations, we implemented a radially-symmetric Mars model with a 110 km thick crust. For this 1D model, we successfully benchmarked the 3D seismic wave propagation solver SPECFEM3D_GLOBE against the 2D axisymmetric wave propagation solver AxiSEM at periods down to 10 s. We also present higher-resolution body-wave simulations with AxiSEM down to 1 s in a model with a more complex 1D crust, revealing wave propagation effects that would have been difficult to interpret based on raymore » theory. For 3D global simulations based on SPECFEM3D_GLOBE, we superimposed 3D crustal thickness variations capturing the distinct crustal dichotomy between Mars’ northern and southern hemispheres, as well as topography, ellipticity, gravity, and rotation. The global simulations clearly indicate that the 3D crust speeds up body waves compared to the reference 1D model, whereas it significantly changes surface waveforms and their dispersive character depending on its thickness. We also perform regional simulations with the solver SES3D based on 3D crustal models derived from surface composition, thereby addressing the effects of various distinct crustal features down to 2 s. The regional simulations confirm the strong effects of crustal variations on waveforms. Finally, we conclude that the numerical tools are ready for examining more scenarios, including various other seismic models and sources.« less

Simulations of Seismic Wave Propagation on Mars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozdağ, Ebru; Ruan, Youyi; Metthez, Nathan

In this paper, we present global and regional synthetic seismograms computed for 1D and 3D Mars models based on the spectral-element method. For global simulations, we implemented a radially-symmetric Mars model with a 110 km thick crust. For this 1D model, we successfully benchmarked the 3D seismic wave propagation solver SPECFEM3D_GLOBE against the 2D axisymmetric wave propagation solver AxiSEM at periods down to 10 s. We also present higher-resolution body-wave simulations with AxiSEM down to 1 s in a model with a more complex 1D crust, revealing wave propagation effects that would have been difficult to interpret based on raymore » theory. For 3D global simulations based on SPECFEM3D_GLOBE, we superimposed 3D crustal thickness variations capturing the distinct crustal dichotomy between Mars’ northern and southern hemispheres, as well as topography, ellipticity, gravity, and rotation. The global simulations clearly indicate that the 3D crust speeds up body waves compared to the reference 1D model, whereas it significantly changes surface waveforms and their dispersive character depending on its thickness. We also perform regional simulations with the solver SES3D based on 3D crustal models derived from surface composition, thereby addressing the effects of various distinct crustal features down to 2 s. The regional simulations confirm the strong effects of crustal variations on waveforms. Finally, we conclude that the numerical tools are ready for examining more scenarios, including various other seismic models and sources.« less

Benchmarking specialty hospitals, a scoping review on theory and practice.

PubMed

Wind, A; van Harten, W H

2017-04-04

Although benchmarking may improve hospital processes, research on this subject is limited. The aim of this study was to provide an overview of publications on benchmarking in specialty hospitals and a description of study characteristics. We searched PubMed and EMBASE for articles published in English in the last 10 years. Eligible articles described a project stating benchmarking as its objective and involving a specialty hospital or specific patient category; or those dealing with the methodology or evaluation of benchmarking. Of 1,817 articles identified in total, 24 were included in the study. Articles were categorized into: pathway benchmarking, institutional benchmarking, articles on benchmark methodology or -evaluation and benchmarking using a patient registry. There was a large degree of variability:(1) study designs were mostly descriptive and retrospective; (2) not all studies generated and showed data in sufficient detail; and (3) there was variety in whether a benchmarking model was just described or if quality improvement as a consequence of the benchmark was reported upon. Most of the studies that described a benchmark model described the use of benchmarking partners from the same industry category, sometimes from all over the world. Benchmarking seems to be more developed in eye hospitals, emergency departments and oncology specialty hospitals. Some studies showed promising improvement effects. However, the majority of the articles lacked a structured design, and did not report on benchmark outcomes. In order to evaluate the effectiveness of benchmarking to improve quality in specialty hospitals, robust and structured designs are needed including a follow up to check whether the benchmark study has led to improvements.

Evaluation of cloud-resolving model simulations of midlatitude cirrus with ARM and A-train observations

DOE PAGES

Muhlbauer, A.; Ackerman, T. P.; Lawson, R. P.; ...

2015-07-14

Cirrus clouds are ubiquitous in the upper troposphere and still constitute one of the largest uncertainties in climate predictions. Our paper evaluates cloud-resolving model (CRM) and cloud system-resolving model (CSRM) simulations of a midlatitude cirrus case with comprehensive observations collected under the auspices of the Atmospheric Radiation Measurements (ARM) program and with spaceborne observations from the National Aeronautics and Space Administration A-train satellites. The CRM simulations are driven with periodic boundary conditions and ARM forcing data, whereas the CSRM simulations are driven by the ERA-Interim product. Vertical profiles of temperature, relative humidity, and wind speeds are reasonably well simulated bymore » the CSRM and CRM, but there are remaining biases in the temperature, wind speeds, and relative humidity, which can be mitigated through nudging the model simulations toward the observed radiosonde profiles. Simulated vertical velocities are underestimated in all simulations except in the CRM simulations with grid spacings of 500 m or finer, which suggests that turbulent vertical air motions in cirrus clouds need to be parameterized in general circulation models and in CSRM simulations with horizontal grid spacings on the order of 1 km. The simulated ice water content and ice number concentrations agree with the observations in the CSRM but are underestimated in the CRM simulations. The underestimation of ice number concentrations is consistent with the overestimation of radar reflectivity in the CRM simulations and suggests that the model produces too many large ice particles especially toward the cloud base. Simulated cloud profiles are rather insensitive to perturbations in the initial conditions or the dimensionality of the model domain, but the treatment of the forcing data has a considerable effect on the outcome of the model simulations. Despite considerable progress in observations and microphysical parameterizations, simulating the microphysical, macrophysical, and radiative properties of cirrus remains challenging. Comparing model simulations with observations from multiple instruments and observational platforms is important for revealing model deficiencies and for providing rigorous benchmarks. But, there still is considerable need for reducing observational uncertainties and providing better observations especially for relative humidity and for the size distribution and chemical composition of aerosols in the upper troposphere.« less

Comparing Hospital Processes and Outcomes in California Medicare Beneficiaries: Simulation Prompts Reconsideration

PubMed Central

Escobar, Gabriel J; Baker, Jennifer M; Turk, Benjamin J; Draper, David; Liu, Vincent; Kipnis, Patricia

2017-01-01

Introduction This article is not a traditional research report. It describes how conducting a specific set of benchmarking analyses led us to broader reflections on hospital benchmarking. We reexamined an issue that has received far less attention from researchers than in the past: How variations in the hospital admission threshold might affect hospital rankings. Considering this threshold made us reconsider what benchmarking is and what future benchmarking studies might be like. Although we recognize that some of our assertions are speculative, they are based on our reading of the literature and previous and ongoing data analyses being conducted in our research unit. We describe the benchmarking analyses that led to these reflections. Objectives The Centers for Medicare and Medicaid Services’ Hospital Compare Web site includes data on fee-for-service Medicare beneficiaries but does not control for severity of illness, which requires physiologic data now available in most electronic medical records. To address this limitation, we compared hospital processes and outcomes among Kaiser Permanente Northern California’s (KPNC) Medicare Advantage beneficiaries and non-KPNC California Medicare beneficiaries between 2009 and 2010. Methods We assigned a simulated severity of illness measure to each record and explored the effect of having the additional information on outcomes. Results We found that if the admission severity of illness in non-KPNC hospitals increased, KPNC hospitals’ mortality performance would appear worse; conversely, if admission severity at non-KPNC hospitals’ decreased, KPNC hospitals’ performance would appear better. Conclusion Future hospital benchmarking should consider the impact of variation in admission thresholds. PMID:29035176

Online collaboration and model sharing in volcanology via VHub.org

NASA Astrophysics Data System (ADS)

Valentine, G.; Patra, A. K.; Bajo, J. V.; Bursik, M. I.; Calder, E.; Carn, S. A.; Charbonnier, S. J.; Connor, C.; Connor, L.; Courtland, L. M.; Gallo, S.; Jones, M.; Palma Lizana, J. L.; Moore-Russo, D.; Renschler, C. S.; Rose, W. I.

2013-12-01

VHub (short for VolcanoHub, and accessible at vhub.org) is an online platform for barrier free access to high end modeling and simulation and collaboration in research and training related to volcanoes, the hazards they pose, and risk mitigation. The underlying concept is to provide a platform, building upon the successful HUBzero software infrastructure (hubzero.org), that enables workers to collaborate online and to easily share information, modeling and analysis tools, and educational materials with colleagues around the globe. Collaboration occurs around several different points: (1) modeling and simulation; (2) data sharing; (3) education and training; (4) volcano observatories; and (5) project-specific groups. VHub promotes modeling and simulation in two ways: (1) some models can be implemented on VHub for online execution. VHub can provide a central warehouse for such models that should result in broader dissemination. VHub also provides a platform that supports the more complex CFD models by enabling the sharing of code development and problem-solving knowledge, benchmarking datasets, and the development of validation exercises. VHub also provides a platform for sharing of data and datasets. The VHub development team is implementing the iRODS data sharing middleware (see irods.org). iRODS allows a researcher to access data that are located at participating data sources around the world (a cloud of data) as if the data were housed in a single virtual database. Projects associated with VHub are also going to introduce the use of data driven workflow tools to support the use of multistage analysis processes where computing and data are integrated for model validation, hazard analysis etc. Audio-video recordings of seminars, PowerPoint slide sets, and educational simulations are all items that can be placed onto VHub for use by the community or by selected collaborators. An important point is that the manager of a given educational resource (or any other resource, such as a dataset or a model) can control the privacy of that resource, ranging from private (only accessible by, and known to, specific collaborators) to completely public. VHub is a very useful platform for project-specific collaborations. With a group site on VHub collaborators share documents, datasets, maps, and have ongoing discussions using the discussion board function. VHub is funded by the U.S. National Science Foundation, and is participating in development of larger earth-science cyberinfrastructure initiatives (EarthCube), as well as supporting efforts such as the Global Volcano Model. Emerging VHub-facilitated efforts include model benchmarking, collaborative code development, and growth in online modeling tools.

Electron-beam-ion-source (EBIS) modeling progress at FAR-TECH, Inc

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, J. S., E-mail: kim@far-tech.com; Zhao, L., E-mail: kim@far-tech.com; Spencer, J. A., E-mail: kim@far-tech.com

FAR-TECH, Inc. has been developing a numerical modeling tool for Electron-Beam-Ion-Sources (EBISs). The tool consists of two codes. One is the Particle-Beam-Gun-Simulation (PBGUNS) code to simulate a steady state electron beam and the other is the EBIS-Particle-In-Cell (EBIS-PIC) code to simulate ion charge breeding with the electron beam. PBGUNS, a 2D (r,z) electron gun and ion source simulation code, has been extended for efficient modeling of EBISs and the work was presented previously. EBIS-PIC is a space charge self-consistent PIC code and is written to simulate charge breeding in an axisymmetric 2D (r,z) device allowing for full three-dimensional ion dynamics.more » This 2D code has been successfully benchmarked with Test-EBIS measurements at Brookhaven National Laboratory. For long timescale (< tens of ms) ion charge breeding, the 2D EBIS-PIC simulations take a long computational time making the simulation less practical. Most of the EBIS charge breeding, however, may be modeled in 1D (r) as the axial dependence of the ion dynamics may be ignored in the trap. Where 1D approximations are valid, simulations of charge breeding in an EBIS over long time scales become possible, using EBIS-PIC together with PBGUNS. Initial 1D results are presented. The significance of the magnetic field to ion dynamics, ion cooling effects due to collisions with neutral gas, and the role of Coulomb collisions are presented.« less

Benchmarking of HEU Mental Annuli Critical Assemblies with Internally Reflected Graphite Cylinder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiaobo, Liu; Bess, John D.; Marshall, Margaret A.

Three experimental configurations of critical assemblies, performed in 1963 at the Oak Ridge Critical Experiment Facility, which are assembled using three different diameter HEU annuli (15-9 inches, 15-7 inches and 13-7 inches) metal annuli with internally reflected graphite cylinder are evaluated and benchmarked. The experimental uncertainties which are 0.00055, 0.00055 and 0.00055 respectively, and biases to the detailed benchmark models which are -0.00179, -0.00189 and -0.00114 respectively, were determined, and the experimental benchmark keff results were obtained for both detailed and simplified model. The calculation results for both detailed and simplified models using MCNP6-1.0 and ENDF VII.1 agree well tomore » the benchmark experimental results with a difference of less than 0.2%. These are acceptable benchmark experiments for inclusion in the ICSBEP Handbook.« less

The challenges of numerically simulating analogue brittle thrust wedges

NASA Astrophysics Data System (ADS)

Buiter, Susanne; Ellis, Susan

2017-04-01

Fold-and-thrust belts and accretionary wedges form when sedimentary and crustal rocks are compressed into thrusts and folds in the foreland of an orogen or at a subduction trench. For over a century, analogue models have been used to investigate the deformation characteristics of such brittle wedges. These models predict wedge shapes that agree with analytical critical taper theory and internal deformation structures that well resemble natural observations. In a series of comparison experiments for thrust wedges, called the GeoMod2004 (1,2) and GeoMod2008 (3,4) experiments, it was shown that different numerical solution methods successfully reproduce sandbox thrust wedges. However, the GeoMod2008 benchmark also pointed to the difficulties of representing frictional boundary conditions and sharp velocity discontinuities with continuum numerical methods, in addition to the well-known challenges of numerical plasticity. Here we show how details in the numerical implementation of boundary conditions can substantially impact numerical wedge deformation. We consider experiment 1 of the GeoMod2008 brittle thrust wedge benchmarks. This experiment examines a triangular thrust wedge in the stable field of critical taper theory that should remain stable, that is, without internal deformation, when sliding over a basal frictional surface. The thrust wedge is translated by lateral displacement of a rigid mobile wall. The corner between the mobile wall and the subsurface is a velocity discontinuity. Using our finite-element code SULEC, we show how different approaches to implementing boundary friction (boundary layer or contact elements) and the velocity discontinuity (various smoothing schemes) can cause the wedge to indeed translate in a stable manner or to undergo internal deformation (which is a fail). We recommend that numerical studies of sandbox setups not only report the details of their implementation of boundary conditions, but also document the modelling attempts that failed. References 1. Buiter and the GeoMod2004 Team, 2006. The numerical sandbox: comparison of model results for a shortening and an extension experiment. Geol. Soc. Lond. Spec. Publ. 253, 29-64 2. Schreurs and the GeoMod2004 Team, 2006. Analogue benchmarks of shortening and extension experiments. Geol. Soc. Lond. Spec. Publ. 253, 1-27 3. Buiter, Schreurs and the GeoMod2008 Team, 2016. Benchmarking numerical models of brittle thrust wedges, J. Struct. Geol. 92, 140-177 4. Schreurs, Buiter and the GeoMod2008 Team, 2016. Benchmarking analogue models of brittle thrust wedges, J. Struct. Geol. 92, 116-13

Assessing 1D Atmospheric Solar Radiative Transfer Models: Interpretation and Handling of Unresolved Clouds.

NASA Astrophysics Data System (ADS)

Barker, H. W.; Stephens, G. L.; Partain, P. T.; Bergman, J. W.; Bonnel, B.; Campana, K.; Clothiaux, E. E.; Clough, S.; Cusack, S.; Delamere, J.; Edwards, J.; Evans, K. F.; Fouquart, Y.; Freidenreich, S.; Galin, V.; Hou, Y.; Kato, S.; Li, J.;  Mlawer, E.;  Morcrette, J.-J.;  O'Hirok, W.;  Räisänen, P.;  Ramaswamy, V.;  Ritter, B.;  Rozanov, E.;  Schlesinger, M.;  Shibata, K.;  Sporyshev, P.;  Sun, Z.;  Wendisch, M.;  Wood, N.;  Yang, F.

2003-08-01

The primary purpose of this study is to assess the performance of 1D solar radiative transfer codes that are used currently both for research and in weather and climate models. Emphasis is on interpretation and handling of unresolved clouds. Answers are sought to the following questions: (i) How well do 1D solar codes interpret and handle columns of information pertaining to partly cloudy atmospheres? (ii) Regardless of the adequacy of their assumptions about unresolved clouds, do 1D solar codes perform as intended?One clear-sky and two plane-parallel, homogeneous (PPH) overcast cloud cases serve to elucidate 1D model differences due to varying treatments of gaseous transmittances, cloud optical properties, and basic radiative transfer. The remaining four cases involve 3D distributions of cloud water and water vapor as simulated by cloud-resolving models. Results for 25 1D codes, which included two line-by-line (LBL) models (clear and overcast only) and four 3D Monte Carlo (MC) photon transport algorithms, were submitted by 22 groups. Benchmark, domain-averaged irradiance profiles were computed by the MC codes. For the clear and overcast cases, all MC estimates of top-of-atmosphere albedo, atmospheric absorptance, and surface absorptance agree with one of the LBL codes to within ±2%. Most 1D codes underestimate atmospheric absorptance by typically 15-25 W m-2 at overhead sun for the standard tropical atmosphere regardless of clouds.Depending on assumptions about unresolved clouds, the 1D codes were partitioned into four genres: (i) horizontal variability, (ii) exact overlap of PPH clouds, (iii) maximum/random overlap of PPH clouds, and (iv) random overlap of PPH clouds. A single MC code was used to establish conditional benchmarks applicable to each genre, and all MC codes were used to establish the full 3D benchmarks. There is a tendency for 1D codes to cluster near their respective conditional benchmarks, though intragenre variances typically exceed those for the clear and overcast cases. The majority of 1D codes fall into the extreme category of maximum/random overlap of PPH clouds and thus generally disagree with full 3D benchmark values. Given the fairly limited scope of these tests and the inability of any one code to perform extremely well for all cases begs the question that a paradigm shift is due for modeling 1D solar fluxes for cloudy atmospheres.

Benchmarking Multilayer-HySEA model for landslide generated tsunami. HTHMP validation process.

NASA Astrophysics Data System (ADS)

Macias, J.; Escalante, C.; Castro, M. J.

2017-12-01

Landslide tsunami hazard may be dominant along significant parts of the coastline around the world, in particular in the USA, as compared to hazards from other tsunamigenic sources. This fact motivated NTHMP about the need of benchmarking models for landslide generated tsunamis, following the same methodology already used for standard tsunami models when the source is seismic. To perform the above-mentioned validation process, a set of candidate benchmarks were proposed. These benchmarks are based on a subset of available laboratory data sets for solid slide experiments and deformable slide experiments, and include both submarine and subaerial slides. A benchmark based on a historic field event (Valdez, AK, 1964) close the list of proposed benchmarks. A total of 7 benchmarks. The Multilayer-HySEA model including non-hydrostatic effects has been used to perform all the benchmarking problems dealing with laboratory experiments proposed in the workshop that was organized at Texas A&M University - Galveston, on January 9-11, 2017 by NTHMP. The aim of this presentation is to show some of the latest numerical results obtained with the Multilayer-HySEA (non-hydrostatic) model in the framework of this validation effort.Acknowledgements. This research has been partially supported by the Spanish Government Research project SIMURISK (MTM2015-70490-C02-01-R) and University of Malaga, Campus de Excelencia Internacional Andalucía Tech. The GPU computations were performed at the Unit of Numerical Methods (University of Malaga).

Characterization and Compensation of Network-Level Anomalies in Mixed-Signal Neuromorphic Modeling Platforms

PubMed Central

Petrovici, Mihai A.; Vogginger, Bernhard; Müller, Paul; Breitwieser, Oliver; Lundqvist, Mikael; Muller, Lyle; Ehrlich, Matthias; Destexhe, Alain; Lansner, Anders; Schüffny, René; Schemmel, Johannes; Meier, Karlheinz

2014-01-01

Advancing the size and complexity of neural network models leads to an ever increasing demand for computational resources for their simulation. Neuromorphic devices offer a number of advantages over conventional computing architectures, such as high emulation speed or low power consumption, but this usually comes at the price of reduced configurability and precision. In this article, we investigate the consequences of several such factors that are common to neuromorphic devices, more specifically limited hardware resources, limited parameter configurability and parameter variations due to fixed-pattern noise and trial-to-trial variability. Our final aim is to provide an array of methods for coping with such inevitable distortion mechanisms. As a platform for testing our proposed strategies, we use an executable system specification (ESS) of the BrainScaleS neuromorphic system, which has been designed as a universal emulation back-end for neuroscientific modeling. We address the most essential limitations of this device in detail and study their effects on three prototypical benchmark network models within a well-defined, systematic workflow. For each network model, we start by defining quantifiable functionality measures by which we then assess the effects of typical hardware-specific distortion mechanisms, both in idealized software simulations and on the ESS. For those effects that cause unacceptable deviations from the original network dynamics, we suggest generic compensation mechanisms and demonstrate their effectiveness. Both the suggested workflow and the investigated compensation mechanisms are largely back-end independent and do not require additional hardware configurability beyond the one required to emulate the benchmark networks in the first place. We hereby provide a generic methodological environment for configurable neuromorphic devices that are targeted at emulating large-scale, functional neural networks. PMID:25303102

Characterization and compensation of network-level anomalies in mixed-signal neuromorphic modeling platforms.

PubMed

Petrovici, Mihai A; Vogginger, Bernhard; Müller, Paul; Breitwieser, Oliver; Lundqvist, Mikael; Muller, Lyle; Ehrlich, Matthias; Destexhe, Alain; Lansner, Anders; Schüffny, René; Schemmel, Johannes; Meier, Karlheinz

2014-01-01

Advancing the size and complexity of neural network models leads to an ever increasing demand for computational resources for their simulation. Neuromorphic devices offer a number of advantages over conventional computing architectures, such as high emulation speed or low power consumption, but this usually comes at the price of reduced configurability and precision. In this article, we investigate the consequences of several such factors that are common to neuromorphic devices, more specifically limited hardware resources, limited parameter configurability and parameter variations due to fixed-pattern noise and trial-to-trial variability. Our final aim is to provide an array of methods for coping with such inevitable distortion mechanisms. As a platform for testing our proposed strategies, we use an executable system specification (ESS) of the BrainScaleS neuromorphic system, which has been designed as a universal emulation back-end for neuroscientific modeling. We address the most essential limitations of this device in detail and study their effects on three prototypical benchmark network models within a well-defined, systematic workflow. For each network model, we start by defining quantifiable functionality measures by which we then assess the effects of typical hardware-specific distortion mechanisms, both in idealized software simulations and on the ESS. For those effects that cause unacceptable deviations from the original network dynamics, we suggest generic compensation mechanisms and demonstrate their effectiveness. Both the suggested workflow and the investigated compensation mechanisms are largely back-end independent and do not require additional hardware configurability beyond the one required to emulate the benchmark networks in the first place. We hereby provide a generic methodological environment for configurable neuromorphic devices that are targeted at emulating large-scale, functional neural networks.

Preliminary SAGE Simulations of Volcanic Jets Into a Stratified Atmosphere

NASA Astrophysics Data System (ADS)

Peterson, A. H.; Wohletz, K. H.; Ogden, D. E.; Gisler, G. R.; Glatzmaier, G. A.

2007-12-01

The SAGE (SAIC Adaptive Grid Eulerian) code employs adaptive mesh refinement in solving Eulerian equations of complex fluid flow desirable for simulation of volcanic eruptions. The goal of modeling volcanic eruptions is to better develop a code's predictive capabilities in order to understand the dynamics that govern the overall behavior of real eruption columns. To achieve this goal, we focus on the dynamics of underexpended jets, one of the fundamental physical processes important to explosive eruptions. Previous simulations of laboratory jets modeled in cylindrical coordinates were benchmarked with simulations in CFDLib (Los Alamos National Laboratory), which solves the full Navier-Stokes equations (includes viscous stress tensor), and showed close agreement, indicating that adaptive mesh refinement used in SAGE may offset the need for explicit calculation of viscous dissipation.We compare gas density contours of these previous simulations with the same initial conditions in cylindrical and Cartesian geometries to laboratory experiments to determine both the validity of the model and the robustness of the code. The SAGE results in both geometries are within several percent of the experiments for position and density of the incident (intercepting) and reflected shocks, slip lines, shear layers, and Mach disk. To expand our study into a volcanic regime, we simulate large-scale jets in a stratified atmosphere to establish the code's ability to model a sustained jet into a stable atmosphere.

Improving predictions of large scale soil carbon dynamics: Integration of fine-scale hydrological and biogeochemical processes, scaling, and benchmarking

NASA Astrophysics Data System (ADS)

Riley, W. J.; Dwivedi, D.; Ghimire, B.; Hoffman, F. M.; Pau, G. S. H.; Randerson, J. T.; Shen, C.; Tang, J.; Zhu, Q.

2015-12-01

Numerical model representations of decadal- to centennial-scale soil-carbon dynamics are a dominant cause of uncertainty in climate change predictions. Recent attempts by some Earth System Model (ESM) teams to integrate previously unrepresented soil processes (e.g., explicit microbial processes, abiotic interactions with mineral surfaces, vertical transport), poor performance of many ESM land models against large-scale and experimental manipulation observations, and complexities associated with spatial heterogeneity highlight the nascent nature of our community's ability to accurately predict future soil carbon dynamics. I will present recent work from our group to develop a modeling framework to integrate pore-, column-, watershed-, and global-scale soil process representations into an ESM (ACME), and apply the International Land Model Benchmarking (ILAMB) package for evaluation. At the column scale and across a wide range of sites, observed depth-resolved carbon stocks and their 14C derived turnover times can be explained by a model with explicit representation of two microbial populations, a simple representation of mineralogy, and vertical transport. Integrating soil and plant dynamics requires a 'process-scaling' approach, since all aspects of the multi-nutrient system cannot be explicitly resolved at ESM scales. I will show that one approach, the Equilibrium Chemistry Approximation, improves predictions of forest nitrogen and phosphorus experimental manipulations and leads to very different global soil carbon predictions. Translating model representations from the site- to ESM-scale requires a spatial scaling approach that either explicitly resolves the relevant processes, or more practically, accounts for fine-resolution dynamics at coarser scales. To that end, I will present recent watershed-scale modeling work that applies reduced order model methods to accurately scale fine-resolution soil carbon dynamics to coarse-resolution simulations. Finally, we contend that creating believable soil carbon predictions requires a robust, transparent, and community-available benchmarking framework. I will present an ILAMB evaluation of several of the above-mentioned approaches in ACME, and attempt to motivate community adoption of this evaluation approach.

Turbulent flow separation in three-dimensional asymmetric diffusers

NASA Astrophysics Data System (ADS)

Jeyapaul, Elbert

2011-12-01

Turbulent three-dimensional flow separation is more complicated than 2-D. The physics of the flow is not well understood. Turbulent flow separation is nearly independent of the Reynolds number, and separation in 3-D occurs at singular points and along convergence lines emanating from these points. Most of the engineering turbulence research is driven by the need to gain knowledge of the flow field that can be used to improve modeling predictions. This work is motivated by the need for a detailed study of 3-D separation in asymmetric diffusers, to understand the separation phenomena using eddy-resolving simulation methods, assess the predictability of existing RANS turbulence models and propose modeling improvements. The Cherry diffuser has been used as a benchmark. All existing linear eddy-viscosity RANS models k--o SST,k--epsilon and v2- f fail in predicting such flows, predicting separation on the wrong side. The geometry has a doubly-sloped wall, with the other two walls orthogonal to each other and aligned with the diffuser inlet giving the diffuser an asymmetry. The top and side flare angles are different and this gives rise to different pressure gradient in each transverse direction. Eddyresolving simulations using the Scale adaptive simulation (SAS) and Large Eddy Simulation (LES) method have been used to predict separation in benchmark diffuser and validated. A series of diffusers with the same configuration have been generated, each having the same streamwise pressure gradient and parametrized only by the inlet aspect ratio. The RANS models were put to test and the flow physics explored using SAS-generated flow field. The RANS model indicate a transition in separation surface from top sloped wall to the side sloped wall at an inlet aspect ratio much lower than observed in LES results. This over-sensitivity of RANS models to transverse pressure gradients is due to lack of anisotropy in the linear Reynolds stress formulation. The complexity of the flow separation is due to effects of lateral straining, streamline curvature, secondary flow of second kind, transverse pressure gradient on turbulence. Resolving these effects is possible with anisotropy turbulence models as the Explicit Algebraic Reynolds stress model (EARSM). This model has provided accurate prediction of streamwise and transverse velocity, however the wall pressure is under predicted. An improved EARSM model is developed by correcting the coefficients, which predicts a more accurate wall pressure. There exists scope for improvement of this model, by including convective effects and dynamics of velocity gradient invariants.

Cyber-Based Turbulent Combustion Simulation

DTIC Science & Technology

2012-02-28

flame thickness by comparing with benchmark of AFRL/RZ ( UNICORN ) suppressing the oscillatory numerical behavior. These improvements in numerical...fraction with the benchmark results of AFRL/RZ. This validating base is generated by the UNICORN program on the finest mesh available and the local...shared kinematic and thermodynamic data from the UNICORN program. The most important and meaningful conclusion can be drawn from this comparison is

Probabilistically modeling lava flows with MOLASSES

NASA Astrophysics Data System (ADS)

Richardson, J. A.; Connor, L.; Connor, C.; Gallant, E.

2017-12-01

Modeling lava flows through Cellular Automata methods enables a computationally inexpensive means to quickly forecast lava flow paths and ultimate areal extents. We have developed a lava flow simulator, MOLASSES, that forecasts lava flow inundation over an elevation model from a point source eruption. This modular code can be implemented in a deterministic fashion with given user inputs that will produce a single lava flow simulation. MOLASSES can also be implemented in a probabilistic fashion where given user inputs define parameter distributions that are randomly sampled to create many lava flow simulations. This probabilistic approach enables uncertainty in input data to be expressed in the model results and MOLASSES outputs a probability map of inundation instead of a determined lava flow extent. Since the code is comparatively fast, we use it probabilistically to investigate where potential vents are located that may impact specific sites and areas, as well as the unconditional probability of lava flow inundation of sites or areas from any vent. We have validated the MOLASSES code to community-defined benchmark tests and to the real world lava flows at Tolbachik (2012-2013) and Pico do Fogo (2014-2015). To determine the efficacy of the MOLASSES simulator at accurately and precisely mimicking the inundation area of real flows, we report goodness of fit using both model sensitivity and the Positive Predictive Value, the latter of which is a Bayesian posterior statistic. Model sensitivity is often used in evaluating lava flow simulators, as it describes how much of the lava flow was successfully modeled by the simulation. We argue that the positive predictive value is equally important in determining how good a simulator is, as it describes the percentage of the simulation space that was actually inundated by lava.

Quantitative assessment of AOD from 17 CMIP5 models based on satellite-derived AOD over India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Misra, Amit; Kanawade, Vijay P.; Tripathi, Sachchida Nand

Aerosol optical depth (AOD) values from 17 CMIP5 models are compared with Moderate Resolution Imaging Spectroradiometer (MODIS) and Multiangle Imaging Spectroradiometer (MISR) derived AODs over India. The objective is to identify the cases of successful AOD simulation by CMIP5 models, considering satellite-derived AOD as a benchmark. Six years of AOD data (2000–2005) from MISR and MODIS are processed to create quality-assured gridded AOD maps over India, which are compared with corresponding maps of 17 CMIP5 models at the same grid resolution. Intercomparison of model and satellite data shows that model-AOD is better correlated with MISR-derived AOD than MODIS. The correlation between model-AOD andmore » MISR-AOD is used to segregate the models into three categories identifying their performance in simulating the AOD over India. Maps of correlation between model-AOD and MISR-/MODIS-AOD are generated to provide quantitative information about the intercomparison. The two sets of data are examined for different seasons and years to examine the seasonal and interannual variation in the correlation coefficients. In conclusion, latitudinal and longitudinal variations in AOD as simulated by models are also examined and compared with corresponding variations observed by satellites.« less

Quantitative assessment of AOD from 17 CMIP5 models based on satellite-derived AOD over India

DOE PAGES

Misra, Amit; Kanawade, Vijay P.; Tripathi, Sachchida Nand

2016-08-03

Aerosol optical depth (AOD) values from 17 CMIP5 models are compared with Moderate Resolution Imaging Spectroradiometer (MODIS) and Multiangle Imaging Spectroradiometer (MISR) derived AODs over India. The objective is to identify the cases of successful AOD simulation by CMIP5 models, considering satellite-derived AOD as a benchmark. Six years of AOD data (2000–2005) from MISR and MODIS are processed to create quality-assured gridded AOD maps over India, which are compared with corresponding maps of 17 CMIP5 models at the same grid resolution. Intercomparison of model and satellite data shows that model-AOD is better correlated with MISR-derived AOD than MODIS. The correlation between model-AOD andmore » MISR-AOD is used to segregate the models into three categories identifying their performance in simulating the AOD over India. Maps of correlation between model-AOD and MISR-/MODIS-AOD are generated to provide quantitative information about the intercomparison. The two sets of data are examined for different seasons and years to examine the seasonal and interannual variation in the correlation coefficients. In conclusion, latitudinal and longitudinal variations in AOD as simulated by models are also examined and compared with corresponding variations observed by satellites.« less

Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups.

PubMed

Alonzo, Frédéric; Hertel-Aas, Turid; Real, Almudena; Lance, Emilie; Garcia-Sanchez, Laurent; Bradshaw, Clare; Vives I Batlle, Jordi; Oughton, Deborah H; Garnier-Laplace, Jacqueline

2016-02-01

In this study, we modelled population responses to chronic external gamma radiation in 12 laboratory species (including aquatic and soil invertebrates, fish and terrestrial mammals). Our aim was to compare radiosensitivity between individual and population endpoints and to examine how internationally proposed benchmarks for environmental radioprotection protected species against various risks at the population level. To do so, we used population matrix models, combining life history and chronic radiotoxicity data (derived from laboratory experiments and described in the literature and the FREDERICA database) to simulate changes in population endpoints (net reproductive rate R0, asymptotic population growth rate λ, equilibrium population size Neq) for a range of dose rates. Elasticity analyses of models showed that population responses differed depending on the affected individual endpoint (juvenile or adult survival, delay in maturity or reduction in fecundity), the considered population endpoint (R0, λ or Neq) and the life history of the studied species. Among population endpoints, net reproductive rate R0 showed the lowest EDR10 (effective dose rate inducing 10% effect) in all species, with values ranging from 26 μGy h(-1) in the mouse Mus musculus to 38,000 μGy h(-1) in the fish Oryzias latipes. For several species, EDR10 for population endpoints were lower than the lowest EDR10 for individual endpoints. Various population level risks, differing in severity for the population, were investigated. Population extinction (predicted when radiation effects caused population growth rate λ to decrease below 1, indicating that no population growth in the long term) was predicted for dose rates ranging from 2700 μGy h(-1) in fish to 12,000 μGy h(-1) in soil invertebrates. A milder risk, that population growth rate λ will be reduced by 10% of the reduction causing extinction, was predicted for dose rates ranging from 24 μGy h(-1) in mammals to 1800 μGy h(-1) in soil invertebrates. These predictions suggested that proposed reference benchmarks from the literature for different taxonomic groups protected all simulated species against population extinction. A generic reference benchmark of 10 μGy h(-1) protected all simulated species against 10% of the effect causing population extinction. Finally, a risk of pseudo-extinction was predicted from 2.0 μGy h(-1) in mammals to 970 μGy h(-1) in soil invertebrates, representing a slight but statistically significant population decline, the importance of which remains to be evaluated in natural settings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Benchmarking an Unstructured-Grid Model for Tsunami Current Modeling

NASA Astrophysics Data System (ADS)

Zhang, Yinglong J.; Priest, George; Allan, Jonathan; Stimely, Laura

2016-12-01

We present model results derived from a tsunami current benchmarking workshop held by the NTHMP (National Tsunami Hazard Mitigation Program) in February 2015. Modeling was undertaken using our own 3D unstructured-grid model that has been previously certified by the NTHMP for tsunami inundation. Results for two benchmark tests are described here, including: (1) vortex structure in the wake of a submerged shoal and (2) impact of tsunami waves on Hilo Harbor in the 2011 Tohoku event. The modeled current velocities are compared with available lab and field data. We demonstrate that the model is able to accurately capture the velocity field in the two benchmark tests; in particular, the 3D model gives a much more accurate wake structure than the 2D model for the first test, with the root-mean-square error and mean bias no more than 2 cm s-1 and 8 mm s-1, respectively, for the modeled velocity.

Benchmarking of Advanced Control Strategies for a Simulated Hydroelectric System

NASA Astrophysics Data System (ADS)

Finotti, S.; Simani, S.; Alvisi, S.; Venturini, M.

2017-01-01

This paper analyses and develops the design of advanced control strategies for a typical hydroelectric plant during unsteady conditions, performed in the Matlab and Simulink environments. The hydraulic system consists of a high water head and a long penstock with upstream and downstream surge tanks, and is equipped with a Francis turbine. The nonlinear characteristics of hydraulic turbine and the inelastic water hammer effects were considered to calculate and simulate the hydraulic transients. With reference to the control solutions addressed in this work, the proposed methodologies rely on data-driven and model-based approaches applied to the system under monitoring. Extensive simulations and comparisons serve to determine the best solution for the development of the most effective, robust and reliable control tool when applied to the considered hydraulic system.

Celeris: A GPU-accelerated open source software with a Boussinesq-type wave solver for real-time interactive simulation and visualization

NASA Astrophysics Data System (ADS)

Tavakkol, Sasan; Lynett, Patrick

2017-08-01

In this paper, we introduce an interactive coastal wave simulation and visualization software, called Celeris. Celeris is an open source software which needs minimum preparation to run on a Windows machine. The software solves the extended Boussinesq equations using a hybrid finite volume-finite difference method and supports moving shoreline boundaries. The simulation and visualization are performed on the GPU using Direct3D libraries, which enables the software to run faster than real-time. Celeris provides a first-of-its-kind interactive modeling platform for coastal wave applications and it supports simultaneous visualization with both photorealistic and colormapped rendering capabilities. We validate our software through comparison with three standard benchmarks for non-breaking and breaking waves.

Correction of defective pixels for medical and space imagers based on Ising Theory

NASA Astrophysics Data System (ADS)

Cohen, Eliahu; Shnitser, Moriel; Avraham, Tsvika; Hadar, Ofer

2014-09-01

We propose novel models for image restoration based on statistical physics. We investigate the affinity between these fields and describe a framework from which interesting denoising algorithms can be derived: Ising-like models and simulated annealing techniques. When combined with known predictors such as Median and LOCO-I, these models become even more effective. In order to further examine the proposed models we apply them to two important problems: (i) Digital Cameras in space damaged from cosmic radiation. (ii) Ultrasonic medical devices damaged from speckle noise. The results, as well as benchmark and comparisons, suggest in most of the cases a significant gain in PSNR and SSIM in comparison to other filters.

A Benchmark Dataset for SSVEP-Based Brain-Computer Interfaces.

PubMed

Wang, Yijun; Chen, Xiaogang; Gao, Xiaorong; Gao, Shangkai

2017-10-01

This paper presents a benchmark steady-state visual evoked potential (SSVEP) dataset acquired with a 40-target brain- computer interface (BCI) speller. The dataset consists of 64-channel Electroencephalogram (EEG) data from 35 healthy subjects (8 experienced and 27 naïve) while they performed a cue-guided target selecting task. The virtual keyboard of the speller was composed of 40 visual flickers, which were coded using a joint frequency and phase modulation (JFPM) approach. The stimulation frequencies ranged from 8 Hz to 15.8 Hz with an interval of 0.2 Hz. The phase difference between two adjacent frequencies was . For each subject, the data included six blocks of 40 trials corresponding to all 40 flickers indicated by a visual cue in a random order. The stimulation duration in each trial was five seconds. The dataset can be used as a benchmark dataset to compare the methods for stimulus coding and target identification in SSVEP-based BCIs. Through offline simulation, the dataset can be used to design new system diagrams and evaluate their BCI performance without collecting any new data. The dataset also provides high-quality data for computational modeling of SSVEPs. The dataset is freely available fromhttp://bci.med.tsinghua.edu.cn/download.html.