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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Coded Wire Tag and Passive Integrated Transponder Tag Implantations in Juvenile Burbot

Abstract Regional stakeholders in various nations are investigating the restoration of imperiled and extirpated Burbot Lota lota populations via the stocking of hatchery-produced fish. Although stocking programs routinely tag fish for monitoring and evaluation projects, there is currently only limited information available regarding effective tagging techniques for use with juvenile Burbot. We identified two anatomical locations (dorsal muscle and peritoneum) that were suitable for PIT tag implantation and six body sites (snout, periocular region, nape, pectoral fin base, dorsal fin base, and ventral [anal fin base]) that were suitable for coded wire tag batch marking of age-0 Burbot (88–144 mm TL). Our evaluation of these implantation methods generally revealed a high rate of tag retention (>95%) and no significant tagging effects on fish survival or growth. A follow-up study also demonstrated satisfactory mass-marking rates for both tag types. Coded wire tags and PIT tags should provide harmless, affordable, long-term identification of hatchery Burbot juveniles. Received August 27, 2013; accepted December 27, 2013

Ashton, Neil K.↗
DOE OSTI2023

Applications of “Synchrotron Radiation Workshop” Code

The “Synchrotron Radiation Workshop” (SRW) computer code was started in the group of Insertion Devices of the European Synchrotron Radiation Facility in 1997. The idea behind it was to combine in one software library electrodynamics methods for calculating electric fields (and derived characteristics) of synchrotron radiation (SR) generated by relativistic electrons moving in magnetic fields of nearly arbitrary configuration with wave-optics methods for simulating propagation of radiation through optical elements of beamlines. Further, the use of this general approach was initially driven by applications in electron beam diagnostics using SR. However, with time it started to be used for more complicated beamlines of synchrotron light sources, and the use of the code for these applications continues to increase, with the new light sources offering brighter and more coherent x ray beams for wide ranges of experiments in different areas of science.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Correcting for telluric absorption: Methods, case studies, and release of the TelFit code

Ground-based astronomical spectra are contaminated by the Earth's atmosphere to varying degrees in all spectral regions. We present a Python code that can accurately fit a model to the telluric absorption spectrum present in astronomical data, with residuals of ∼3%-5% of the continuum for moderately strong lines. We demonstrate the quality of the correction by fitting the telluric spectrum in a nearly featureless A0V star, HIP 20264, as well as to a series of dwarf M star spectra near the 819 nm sodium doublet. We directly compare the results to an empirical telluric correction of HIP 20264 and find that our model-fitting procedure is at least as good and sometimes more accurate. The telluric correction code, which we make freely available to the astronomical community, can be used as a replacement for telluric standard star observations for many purposes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Cosmic ray transport in heliospheric magnetic structures. I. Modeling background solar wind using the CRONOS magnetohydrodynamic code

The transport of energetic particles such as cosmic rays is governed by the properties of the plasma being traversed. While these properties are rather poorly known for galactic and interstellar plasmas due to the lack of in situ measurements, the heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric transport of energetic particles are structures such as corotating interaction regions, which, due to strongly enhanced magnetic field strengths, turbulence, and associated shocks, can act as diffusion barriers on the one hand, but also as accelerators of low energy CRs on the other hand as well. In a two-fold series of papers, we investigate these effects by modeling inner-heliospheric solar wind conditions with a numerical magnetohydrodynamic (MHD) setup (this paper), which will serve as an input to a transport code employing a stochastic differential equation approach (second paper). In this first paper, we present results from 3D MHD simulations with our code CRONOS: for validation purposes we use analytic boundary conditions and compare with similar work by Pizzo. For a more realistic modeling of solar wind conditions, boundary conditions derived from synoptic magnetograms via the Wang-Sheeley-Arge (WSA) model are utilized, where the potential field modeling is performed with a finite-difference approach in contrast to the traditional spherical harmonics expansion often utilized in the WSA model. Our results are validated by comparing with multi-spacecraft data for ecliptical (STEREO-A/B) and out-of-ecliptic (Ulysses) regions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Tau-REx I: A next generation retrieval code for exoplanetary atmospheres

Spectroscopy of exoplanetary atmospheres has become a well established method for the characterization of extrasolar planets. We here present a novel inverse retrieval code for exoplanetary atmospheres. T-REx(Tau Retrieval for Exoplanets) is a line-by-line radiative transfer fully Bayesian retrieval framework. T-REx includes the following features:(1) the optimized use of molecular line lists from the ExoMol project; (2) an unbiased atmospheric composition prior selection, through custom built pattern recognition software; (3) the use of two independent algorithms to fully sample the Bayesian likelihood space: nested sampling as well as a more classical Markov Chain Monte Carlo approach; (4) iterative Bayesian parameter and model selection using the full Bayesian Evidence as well as the Savage–Dickey Ratio for nested models; and (5) the ability to fully map very large parameter spaces through optimal code parallelization and scalability to cluster computing. In this publication we outline the T-REx framework and demonstrate, using a theoretical hot-Jupiter transmission spectrum, the parameter retrieval and model selection. We investigate the impact of signal-to-noise ratio and spectral resolution on the retrievability of individual model parameters, both in terms of error bars on the temperature and molecular mixing ratios as well as its effect on the model’s global Bayesian evidence.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

LIGHT CURVES OF CORE-COLLAPSE SUPERNOVAE WITH SUBSTANTIAL MASS LOSS USING THE NEW OPEN-SOURCE SUPERNOVA EXPLOSION CODE (SNEC)

We present the SuperNova Explosion Code (SNEC), an open-source Lagrangian code for the hydrodynamics and equilibrium-diffusion radiation transport in the expanding envelopes of supernovae. Given a model of a progenitor star, an explosion energy, and an amount and distribution of radioactive nickel, SNEC generates the bolometric light curve, as well as the light curves in different broad bands assuming blackbody emission. As a first application of SNEC, we consider the explosions of a grid of 15 M{sub ⊙} (at zero-age main sequence, ZAMS) stars whose hydrogen envelopes are stripped to different extents and at different points in their evolution. The resulting light curves exhibit plateaus with durations of ∼20–100 days if ≳1.5–2 M{sub ⊙} of hydrogen-rich material is left and no plateau if less hydrogen-rich material is left. If these shorter plateau lengths are not seen for SNe IIP in nature, it suggests that, at least for ZAMS masses ≲20 M{sub ⊙}, hydrogen mass loss occurs as an all or nothing process. This perhaps points to the important role binary interactions play in generating the observed mass-stripped supernovae (i.e., Type Ib/c events). These light curves are also unlike what is typically seen for SNe IIL, arguing that simply varying the amount of mass loss cannot explain these events. The most stripped models begin to show double-peaked light curves similar to what is often seen for SNe IIb, confirming previous work that these supernovae can come from progenitors that have a small amount of hydrogen and a radius of ∼500 R{sub ⊙}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

AEOLUS: A MARKOV CHAIN MONTE CARLO CODE FOR MAPPING ULTRACOOL ATMOSPHERES. AN APPLICATION ON JUPITER AND BROWN DWARF HST LIGHT CURVES

Deducing the cloud cover and its temporal evolution from the observed planetary spectra and phase curves can give us major insight into the atmospheric dynamics. In this paper, we present Aeolus, a Markov chain Monte Carlo code that maps the structure of brown dwarf and other ultracool atmospheres. We validated Aeolus on a set of unique Jupiter Hubble Space Telescope (HST) light curves. Aeolus accurately retrieves the properties of the major features of the Jovian atmosphere, such as the Great Red Spot and a major 5 μm hot spot. Aeolus is the first mapping code validated on actual observations of a giant planet over a full rotational period. For this study, we applied Aeolus to J- and H-band HST light curves of 2MASS J21392676+0220226 and 2MASS J0136565+093347. Aeolus retrieves three spots at the top of the atmosphere (per observational wavelength) of these two brown dwarfs, with a surface coverage of 21% ± 3% and 20.3% ± 1.5%, respectively. The Jupiter HST light curves will be publicly available via ADS/VIZIR.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

THREE-DIMENSIONAL BOLTZMANN HYDRO CODE FOR CORE COLLAPSE IN MASSIVE STARS. I. SPECIAL RELATIVISTIC TREATMENTS

We propose a novel numerical method for solving multi-dimensional, special relativistic Boltzmann equations for neutrinos coupled with hydrodynamics equations. This method is meant to be applied to simulations of core-collapse supernovae. We handle special relativity in a non-conventional way, taking account of all orders of v/c. Consistent treatment of the advection and collision terms in the Boltzmann equations has been a challenge, which we overcome by employing two different energy grids: Lagrangian remapped and laboratory fixed grids. We conduct a series of basic tests and perform a one-dimensional simulation of core-collapse, bounce, and shock-stall for a 15 M {sub ☉} progenitor model with a minimum but essential set of microphysics. We demonstrate in the latter simulation that our new code is capable of handling all phases in core-collapse supernova. For comparison, a non-relativistic simulation is also conducted with the same code, and we show that they produce qualitatively wrong results in neutrino transfer. Finally, we discuss a possible incorporation of general relativistic effects into our method.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Simulation of neutron emission in neutral beam injection heated plasmas with the real-time code RABBIT

In plasmas heated with deuterium beams a deficit of the expected fusion neutron rate is an indicator of the deterioration of the fast-ion confinement, caused, for instance, by magnetohydrodynamic instabilities. The capability of predicting this deficit during the discharge relies on the availability of real-time estimates of the neutron rate from NBI codes which must be fast and accurate at the same time. Therefore, the recently developed real-time RABBIT code for NBI simulations has been extended to output the distribution function and calculate the neutron emission. After the description of this newly installed diagnostics in RABBIT, benchmarks with NUBEAM, a massively used and validated Monte Carlo NBI solver, are discussed on ASDEX-Upgrade and JET cases. A first application for control-room intershot analysis on DIII-D is presented, and the results are compared on a large database with a slower NUBEAM analysis. Further application possibilities, e.g. for real-time control of Alfvén eigenmodes, are outlined.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Simulation of divertor heat flux width on EAST by BOUT++ transport code

The BOUT++ edge plasma transport code is applied to study the effects of neutral recycling, drifts and heating scheme on edge plasma profiles and the divertor heat flux width of two discharges of the experimental advanced superconducting tokamak (EAST) steady-state H-mode plasmas heated by low hybrid wave (LHW) and neutral beam (NB), respectively. Neutral recycling seems to have played an important role in the plasma density profile. The edge plasma density drops dramatically for the case w/o neutral recycling, while it can be sustained for the case w/ neutral recycling. Drifts are found to have significant influences on edge plasma profiles. Both the amplitude and width of the divertor heat flux are found to have increased a lot due to drifts. The simulated heat flux width w/ drifts for the two discharges shows reasonable agreement with the experiments. However, the width from the simulation and experiment for the LHW heated discharge is much larger than that of the NB heated discharge. Comparison with Goldston's drift-based model and more detailed analysis on the heat flux contributions from drifts versus turbulence show that drifts are the dominant factor in edge plasma transport for both LHW and NB heated discharges, while turbulence may have played a more important role in determining the heat flux width in LHW heated discharges than that in NB heated discharges. This may account for the larger heat flux width in the LHW heated discharge. The magnetic topology and the equilibrium change by the LHW power may also be a potential reason for the larger heat flux width in the LHW heated discharges, which still needs more evidence and studies to support it. Finally, additional SOLPS simulation w/o drifts for the two discharges show reasonable agreement with the counterpart from the BOUT++ simulation, suggesting the two are both suitable codes for EAST edge plasma simulation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Prediction of divertor heat flux width for ITER pre-fusion power operation using BOUT++ transport code

Prediction of divertor heat flux width is performed for the first and the second pre-fusion power operation (PFPO) phases specified in the new ITER research plan using BOUT++ transport code (Li et al 2018 Comput. Phys. Commun.228 69–82). Here the initial plasma profiles inside the separatrix are taken from CORSICA scenario studies. Transport coefficients in transport code are calculated by inverting the plasma profiles inside the separatrix and are assumed to be constants in the scrape-off-layer. An anomalous thermal diffusivity scan is performed with E × B and magnetic drifts. The results in two scenarios identifying two distinct regimes: a drift-dominant regime when diffusivity is smaller than the respective critical thermal diffusivity χ c and a turbulence-dominant regime when diffusivity is larger than it. The Goldston heuristic drift model and the ITPA multi-machine experimental scaling yield a lower limit of the width λ q . From transport simulations, we obtain the critical thermal diffusivity χ c = 0.5 m 2 s –1 for the PFPO-1 scenario with toroidal magnetic field B = 1.77 T and plasma current I p = 5 MA, and χ c = 0.3 m 2 s –1 for the PFPO-2 scenario with toroidal magnetic field B = 2.65 T and plasma current I p = 7.5 MA. Separatrix temperature and collisionality also have a significant impact on the heat flux width in the drift-dominant regime. The investigation clearly yields a scaling for critical thermal diffusivity ${\chi }_{\text{c}}\propto {A}^{1/2}/(Z{\left(1+Z\right)}^{\frac{1}{2}}{B}_{\text{p}}^{2})$ using ITER scenarios with fixed safety factor q 95 , major radius R, aspect ratio R/a, and the separatrix temperature T sep , and establishes the connection with CFETR and C-Mod discharges. This scaling implies that for a given tokamak device with q 95 , R, R/a, and T sep fixed, a reduction of poloidal magnetic field by a factor of 3 leads to a 9 times higher critical value of thermal diffusivity χ c , possibly yielding a transition from turbulence- to drift-dominant regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Kinetic modeling of hot tail runaway electron generation during plasma disruptions using the JOREK code

The generation of runaway electrons (REs) during disruptions poses a significant challenge for the operation of tokamaks. The production of these high-energy electrons can cause substantial damage, particularly when the plasma current is high, making it a critical concern for ITER. For the high-temperature plasmas anticipated in ITER, the primary generation of REs may be dominated by the hot tail mechanism, which consists of the acceleration of hot electrons from the pre-disruption population which have not yet thermalized with the bulk following the rapid cooling of the plasma. To account for the significant 3D effects on RE production, a hot tail modeling framework has been developed within the non-linear 3D extended MHD code JOREK. This paper presents the structure of this framework, which is based on test electrons evolving in MHD fields. The verification of the method shows good agreement with the reference DREAM code for 0D test cases, as well as for axisymmetric simulations of 15 MA ITER H-mode disruption scenarios. Furthermore, a proof-of-principle application to a DIII-D case demonstrates the framework’s capability to capture for the first time the hot tail generation in 3D MHD simulations in realistic geometry. Preliminary results suggest that the production of REs is significantly reduced by stochastic losses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Virtual machine provisioning, code management, and data movement design for the Fermilab HEPCloud Facility

The Fermilab HEPCloud Facility Project has as its goal to extend the current Fermilab facility interface to provide transparent access to disparate resources including commercial and community clouds, grid federations, and HPC centers. This facility enables experiments to perform the full spectrum of computing tasks, including data-intensive simulation and reconstruction. We have evaluated the use of the commercial cloud to provide elasticity to respond to peaks of demand without overprovisioning local resources. Full scale data-intensive workflows have been successfully completed on Amazon Web Services for two High Energy Physics Experiments, CMS and NOνA, at the scale of 58000 simultaneous cores. This paper describes the significant improvements that were made to the virtual machine provisioning system, code caching system, and data movement system to accomplish this work. The virtual image provisioning and contextualization service was extended to multiple AWS regions, and to support experiment-specific data configurations. A prototype Decision Engine was written to determine the optimal availability zone and instance type to run on, minimizing cost and job interruptions. We have deployed a scalable on-demand caching service to deliver code and database information to jobs running on the commercial cloud. It uses the frontiersquid server and CERN VM File System (CVMFS) clients on EC2 instances and utilizes various services provided by AWS to build the infrastructure (stack). We discuss the architecture and load testing benchmarks on the squid servers. We also describe various approaches that were evaluated to transport experimental data to and from the cloud, and the optimal solutions that were used for the bulk of the data transport. Finally, we summarize lessons learned from this scale test, and our future plans to expand and improve the Fermilab HEP Cloud Facility.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Enabling attractive-repulsive potentials in binary-collision-approximation monte-carlo codes for ion-surface interactions

Abstract Binary Collision Approximation (BCA) codes for ion-material interactions, such as SRIM, Tridyn, F-TRIDYN, and SDtrimSP, have historically been limited to screened Coulomb potentials even at low energies due to the difficulty in numerically solving the Distance of Closest Approach (DOCA) problem for attractive-repulsive potentials. Techniques such as direct n-body simulation or modifications to Newton’s method are either prohibitively costly or not guaranteed to work for all potentials. Advanced rootfinding techniques, such as companion matrix solvers, offer a solution. For many attractive-repulsive potentials, however, a companion matrix cannot be used directly, because there is no way to put the associated functions into a monomial basis form. A complementary technique is proxy rootfinding—by finding the best-fit polynomial approximant of a function, the zeros of the approximant can be guaranteed to be close to the zeros of the function. Using the Chebyshev basis and grid offers additional guarantees with regards to the quality of the approximation, the speed of convergence, and the avoidance of Runge’s phenomenon. By finding Chebyshev interpolants and using the Chebyshev-Frobenius companion matrix, the zeros of any real function on a bounded domain can be found. Here we show that using an Adaptive Chebyshev Proxy Rootfinder with Automatic Subdivision (ACPRAS) with appropriate scaling functions, numerical issues presented by attractive-repulsive potentials, including those of scale, can be handled. Using these techniques, we show that it is possible to include any physically reasonable interatomic potential in a BCA code, and to guarantee correctness of the resulting scattering angle calculations.

Materials Science↗
DOE OSTI2021

ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗
DOE OSTI2021

The picasso map-making code: application to a simulation of the QUIJOTE northern sky survey

ABSTRACT Map-making is an important step for the data analysis of cosmic microwave background (CMB) experiments. It consists of converting the data, which are typically a long, complex, and noisy collection of measurements, into a map, which is an image of the observed sky. We present in this paper a new map-making code named picasso (Polarization and Intensity CArtographer for Scanned Sky Observations), which was implemented to construct intensity and polarization maps from the Multi Frequency Instrument (MFI) of the QUIJOTE (Q-U-I Joint TEnerife) CMB polarization experiment. picasso is based on the destriping algorithm, and is suited to address specific issues of ground-based microwave observations, with a technique that allows the fit of a template function in the time domain, during the map-making step. This paper describes the picasso code, validating it with simulations and assessing its performance. For this purpose, we produced realistic simulations of the QUIJOTE-MFI survey of the northern sky (approximately ∼20 000 deg2), and analysed the reconstructed maps with picasso, using real and harmonic space statistics. We show that, for this sky area, picasso is able to reconstruct, with high fidelity, the injected signal, recovering all the scales with ℓ > 10 in TT, EE, and BB. The signal error is better than 0.001 per cent at 20 < ℓ < 200. Finally, we validated some of the methods that will be applied to the real wide-survey data, like the detection of the CMB anisotropies via cross-correlation analyses. Despite that the implementation of picasso is specific for QUIJOTE-MFI data, it could be adapted to other experiments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

EMMA: an adaptive mesh refinement cosmological simulation code with radiative transfer

EMMA is a cosmological simulation code aimed at investigating the reionization epoch. It handles simultaneously collisionless and gas dynamics, as well as radiative transfer physics using a moment-based description with the M1 approximation. Field quantities are stored and computed on an adaptive three-dimensional mesh and the spatial resolution can be dynamically modified based on physically motivated criteria. Physical processes can be coupled at all spatial and temporal scales. We also introduce a new and optional approximation to handle radiation: the light is transported at the resolution of the non-refined grid and only once the dynamics has been fully updated, whereas thermo-chemical processes are still tracked on the refined elements. Such an approximation reduces the overheads induced by the treatment of radiation physics. A suite of standard tests are presented and passed by EMMA, providing a validation for its future use in studies of the reionization epoch. The code is parallel and is able to use graphics processing units (GPUs) to accelerate hydrodynamics and radiative transfer calculations. Depending on the optimizations and the compilers used to generate the CPU reference, global GPU acceleration factors between ×3.9 and ×16.9 can be obtained. As a result, vectorization and transfer operations currently prevent better GPU performance and we expect that future optimizations and hardware evolution will lead to greater accelerations.

79 ASTRONOMY AND ASTROPHYSICS↗