Search NASA⌕ Search

SEARCH · Search NASA

Results for “P CODES”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Quantum closures for neutrino moment transport

A computationally efficient method for calculating the transport of neutrino flavor in simulations is to use angular moments of the neutrino one-body reduced density matrix, i.e., “quantum moments.” As with any moment-based radiation transport method, a closure is needed if the infinite tower of moment evolution equations is truncated. We derive a general parametrization of a quantum closure and the limits the parameters must satisfy in order for the closure to be physical. We then derive from multiangle calculations the evolution of the closure parameters in two test cases which we then progressively insert into a moment evolution code and show how the parameters affect the moment results until the full multiangle results are reproduced. This parametrization paves the way to setting prescriptions for genuine quantum closures adapted to neutrino transport in a range of situations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Electric-field enhancement caused by subwavelength-sized particles located on the surface of multilayer dielectric mirrors

A laser pulse impinging on the surface of an optical component can interact with particles, such as contamination debris, to produce a scattered electric field, which, either by itself or combined with the incident laser field, coherently can significantly increase the local field intensity. This effect can be of critical importance as it can reduce the laser-induced–damage threshold of the affected component. In this work, we use a field-propagation code to improve understanding regarding the factors that determine the magnitude and location of the electric-field enhancement for the case of subwavelength-sized particles located on the surface of multilayer dielectric mirrors.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Equilipy: a python package for calculating phase equilibria

The CALPHAD (CALculation of PHAse Diagram) approach (Nigel Saunders & Miodownik, 1998) provides predictions for thermodynamically stable phases in multicomponent-multiphase materials across a wide range of temperatures. Consequently, the CALPHAD calculations became an essential tool in materials and process design (Luo, 2015). Such design tasks frequently require navigating a high-dimensional space due to multiple components involved in the system. This increasing complexity demands high-throughput CALPHAD calculations, especially in the rapidly evolving field of alloy design. In response to the need, we developed Equilipy an open-source Python package designed for calculating phase equilibria of multicomponent-multiphase systems. Equilipy is specifically tailored for high-throughput CALPHAD calculations, offering parallel computations across multiple processors and nodes with the given NPT input conditions namely elemental compositions (N), pressure (P), and temperature (T). Equilipy utilizes the program structure and Gibbs energy functions from the Fortran-based program, Thermochimica (Piro et al., 2013), with incorporating a new Gibbs energy minimization algorithm. This algorithm, originally developed by Capitani and Brown in 1987 (Capitani & Brown, 1987), has been revised and implemented to enhance the stability and performance of calculations. The Fortran codes are precompiled and interfaced with Python via F2PY, ensuring high computation speed. Benchmark tests shown in Figure 1 demonstrate that Equilipy’s computation speed is comparable to those of established commercial software, TC-Python and PanPython. This result highlights its efficiency and potential applications in various scientific and industrial fields.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Contributions for ENDF/B-VIII.1 Paper

It was discussed at WANDA2020 that some issues were found by the community and users in ENDF/B-VIII.0 covariances after their release. It was mentioned that one issue in testing ENDF/B-VIII.0 covariances was that they were provided by evaluators too late in the β-release phases that insufficient time for thorough testing was available. Therefore, the executive committee requested that first nuclear data covariances should already be delivered for ENDF/B-VIII.1β 1 in February 2023—about half a year earlier than was the case for ENDF/B-VIII.0. This additional time allowed for more stringent testing with LANL’s ENDFtk and CovVal codes, and ORNL’s AMPX code during the release phases. The LLNL covariance testing employed a combination of NJOY, empy tools from EMPIRE, and x4i.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Simulation of Peach Bottom turbine trip transient with RETRAN-3D using BXFGEN

The Peach Bottom 2 Turbine Trip transient is used to evaluate the capabilities and accuracy of coupled 3-D neutronics/thermal hydraulics best estimate calculations for support of safety analysis. Selected results, obtained with RETRAN-3D, are compared to available measurements and benchmark results. The comparisons are analyzed and the application of RETRAN-3D for a best estimate analysis approach within the safety analysis methodology is discussed. Overall, both the thermal-hydraulic and neutronic results show a good comparison to the experimental data, and the model is considered to accurately predict test data. In particular, the initial acoustic response of the main steam line and the subsequent main pressurization stages are well-predicted. During the main pressurization stage, the timing and magnitude of the in-core local pressurization and associated void compression are properly predicted based upon the agreement between local power range monitors (LPRM) predictions upwards, but the shift is slightly underpredicted. This indicates the methodology is well-posed for simulating this class of transient response.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

Error field correction strategies in preparation to MAST-U operation

In magnetic fusion devices, unwanted non-axisymmetric magnetic field perturbations, known as error fields (EF), can have detrimental effects on plasma stability and confinement. Such EFs may originate from several sources, such as axi-symmetric coil misalignments, coil feeds, 3D structures in the wall surrounding the plasma, presence of ferromagnetic materials near the plasma surface, blanket materials in future devices. To minimize their impact on plasma performance and on the available operational space, it is important to identify the EF sources and develop EF control strategies. MAST Upgrade (MAST-U) is a spherical tokamak which will operate in the near future after a series of enhancements from the previous MAST experiment. To deliver a machine with EF amplitude low enough to allow a high quality experimental programme, systematic analysis of the intrinsic EF sources has been carried out for poloidal eld (P) and divertor (D) coils. To deliver a machine with EF amplitude low enough to allow a high quality experimental programme, systematic analysis of the intrinsic EF sources has been carried out for poloidal field (P) and divertor (D) coils, whose magnetic eld measurements were available when writing this paper. Such measurements reveal that P and D coils are 3D deformed and thus are responsible for intrinsic EFs, with mainly n=1 and n=2 toroidal mode numbers. In preparation to MAST-U operation, both passive and active EF control strategies have been adopted for n=1 and n=2 EFs compensation. Passive EF control consisted of installing finely each D and P coil within MAST-U device so as to minimize the intrinsic n=1 EF amplitude. The optimal coil alignment has been determined based on magnetic eld measurements and the corresponding 3D electro-magnetic modelling, and envisaged coil shift and tilt of 3.2 mm and 0.7 mrad, respectively, in the case of P coil named P4. Conversely, active control will be use during MAST-U operation to reduce the n=2 EF which is associated mainly with P4 and P5, as well. Since these coils have been re-used from the MAST device, studies attempting n=2 EF control, based on MAST plasmas, have been modelled utilizing the MARS-F code to interpret experimental results in MAST and to give hints for future n=2 EF control studies in MAST-U. Here, a model-based control set for n=2 EF control has been identified which would allow for the minimization of rotation braking, of the resonant magnetic field at the q=2 and of the plasma displacement in MAST-U, simultaneously.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

EvaluateFlux, VARPOW, VARPEAK, and DIF3DtoVTK Utility Programs for DIF3D

The DIF3D-VARIANT solver is part of the DIF3D code which was developed at ANL for engineering level predictive analysis of nuclear reactor cores. Over the course of the last 20 years, the DIF3D-VARIANT option of DIF3D has become increasingly more used because of improvements in computer memory capabilities and performance. This is beneficial to the users of DIF3D as DIF3D-VARIANT is able to apply both p- and h- spatial mesh refinement strategies in diffusion and transport theory. Given its greater use, utility programs were created to assist in post-processing the DIF3D output. This document discusses the basic execution process of DIF3D and the output files it creates but is primarily focused on being the manual for the utility programs EvaluateFlux, VARPOW, VARPEAK, and DIF3DtoVTK.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

EvaluateFlux, VARPOW, VARPEAK, and DIF3DtoVTK Utility Programs for DIF3D (Rev. 1)

The DIF3D-VARIANT solver is part of the DIF3D code which was developed at ANL for engineering level predictive analysis of nuclear reactor cores. Over the course of the last 20 years, the DIF3D-VARIANT option of DIF3D has become increasingly more used because of improvements in computer memory capabilities and performance. This is beneficial to the users of DIF3D as DIF3D-VARIANT is able to apply both p- and h-spatial mesh refinement strategies in diffusion and transport theory. Given its greater use, utility programs were created to assist in post-processing the DIF3D output. This document discusses the basic execution process of DIF3D and the output files it creates but is primarily focused on being the manual for the utility programs EvaluateFlux, VARPOW, VARPEAK, and DIF3DtoVTK.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals

Current neutrino detectors will observe hundreds to thousands of neutrinos from a Galactic supernovae, and future detectors will increase this yield by an order of magnitude or more. With such a data set comes the potential for a huge increase in our understanding of the explosions of massive stars, nuclear physics under extreme conditions, and the properties of the neutrino. However, there is currently a large gap between supernova simulations and the corresponding signals in neutrino detectors, which will make any comparison between theory and observation very difficult. SNEWPY is an open-source software package which bridges this gap. The SNEWPY code can interface with supernova simulation data to generate from the model either a time series of neutrino spectral fluences at Earth, or the total time-integrated spectral fluence. Data from several hundred simulations of core-collapse, thermonuclear, and pair-instability supernovae is included in the package. This output may then be used by an event generator such as sntools or an event rate calculator such as SNOwGLoBES. Additional routines in the SNEWPY package automate the processing of the generated data through the SNOwGLoBES software and collate its output into the observable channels of each detector. In this paper we describe the contents of the package, the physics behind SNEWPY, the organization of the code, and provide examples of how to make use of its capabilities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals

Current neutrino detectors will observe hundreds to thousands of neutrinos from Galactic supernovae, and future detectors will increase this yield by an order of magnitude or more. With such a data set comes the potential for a huge increase in our understanding of the explosions of massive stars, nuclear physics under extreme conditions, and the properties of the neutrino. However, there is currently a large gap between supernova simulations and the corresponding signals in neutrino detectors, which will make any comparison between theory and observation very difficult. SNEWPY is an open-source software package that bridges this gap. The SNEWPY code can interface with supernova simulation data to generate from the model either a time series of neutrino spectral fluences at Earth, or the total time-integrated spectral fluence. Data from several hundred simulations of core-collapse, thermonuclear, and pair-instability supernovae is included in the package. This output may then be used by an event generator such as sntools or an event rate calculator such as the SuperNova Observatories with General Long Baseline Experiment Simulator (SNOwGLoBES). Additional routines in the SNEWPY package automate the processing of the generated data through the SNOwGLoBES software and collate its output into the observable channels of each detector. In this paper we describe the contents of the package, the physics behind SNEWPY, the organization of the code, and provide examples of how to make use of its capabilities.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Phase-field simulations of fission gas bubble growth and interconnection in U-(Pu)-Zr nuclear fuel

Abstract The growth and interconnection of fission gas bubbles in the hotter central regions of U-(Pu)-Zr nuclear fuel has been simulated with a phase-field model. The Cahn-Hilliard equation was used to represent the two-phase microstructure, with a single defect species. The volume fraction of the bubble phase and surface area of the bubble-matrix interface were determined during growth and interconnection. Surface area increased rapidly during the initial stages of growth, then slowed and finally decreased as bubble interconnection began and coarsening acted to reduce surface area. The fraction of the bubbles vented to a simulation domain boundary, f V , was quantified as a measure of the microstructure’s interconnectivity and plotted as a function of porosity p . The defect species diffusivity was varied; although changes in diffusivity significantly affected the microstructure, the plots of f V vs. p did not change significantly. The percolation threshold p c was calculated to be approximately 0.26, depending on the assumed diffusivity and using an initial bubble number density based on experimental observations. This is slightly smaller than the percolation threshold for continuum percolation of overlapping 3D spheres. The simulation results were used to parameterize two different engineering-scale swelling models for U-(Pu)-Zr in the nuclear fuel performance code BISON.

Aagesen, Larry K. (ORCID:000000034936676X)↗
DOE OSTI2021

First coupled GENE–XGC microturbulence simulations

Covering the core and the edge region of a tokamak, respectively, the two gyrokinetic turbulence codes Gyrokinetic Electromagnetic Numerical Experiment (GENE) and X-point Gyrokinetic Code (XGC) have been successfully coupled by exchanging three-dimensional charge density data needed to solve the gyrokinetic Poisson equation over the entire spatial domain. Certain challenges for the coupling procedure arise from the fact that the two codes employ completely different numerical methods. This includes, in particular, the necessity to introduce mapping procedures for the transfer of data between the unstructured triangular mesh of XGC and the logically rectangular grid (in a combination of real and Fourier space) used by GENE. Constraints on the coupling scheme are also imposed by the use of different time integrators. First, coupled simulations are presented. We have considered collisionless ion temperature gradient turbulence, in both circular and fully shaped plasmas. Coupled simulations successfully reproduce both GENE and XGC reference results, confirming the validity of the code coupling approach toward a whole device model. Here, many lessons learned in the present context, in particular, the need for a coupling procedure as flexible as possible, should be valuable to our and other efforts to couple different kinds of codes in pursuit of a more comprehensive description of complex real-world systems and will drive our further developments of a whole device model for fusion plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Millimeter-wave beam scattering and induced broadening by plasma turbulence in the TCV tokamak

The scattering of millimeter-wave beams from electron density fluctuations and the associated beam broadening are experimentally demonstrated. Using a dedicated setup, instantaneous deflection and (de-)focusing of the beam due to density blobs on the beam path are shown to agree with full-wave simulations. The detected time-averaged wave power transmitted through the turbulent plasma is reproduced by the radiative-transfer model implemented in the WKBeam code, which predicts a ~50% turbulence-induced broadening of the beam cross-section. Finally, the role of core turbulence for the considered geometry is highlighted.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357

Abstract Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CuXASNet: Rapid and accurate prediction of copper L-edge x-ray absorption spectra using machine learning

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu -edge x-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the and edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average mean absolute error of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly predict a large number of -edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal edges.

36 MATERIALS SCIENCE↗
DOE OSTI2021

U.S. Industry Opportunities for Advanced Nuclear Technology Development Phase II (Final Report)

This limited scope study aims at preserving the results of experimental programs for the safety of light water cooled and advanced reactors by locating and documenting, to the extent possible, where the experimental test information for these programs has been archived. The Light Water Reactor Data Preservation Activity Team initially identified seven (7) experimental programs, exceeding the required five (5) in the scope of work, which were determined to be “at risk” of potentially losing valuable data. The seven (7) experimental programs/subject areas identified are (descriptions of each experiment/experience are provided in Section 3.0): 1. FERMI-1 Reactor Accident 2. Fission Product Behavior During the In-Pile Severe Fuel Damage Test SFD I-4 3. Containment Iodine Computer Code Exercise Based on Radioiodine Test Facility (RTF) Experiment 4. Wide Range Piping Integrity Demonstration (WIND) Project 5. Iodine Chemical Research in Canada 6. High Temperature Fission Product Chemistry and Transport in Steam 7. Anything related to radioactive Methyl Iodide.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗