Wide-scale Adoption through Visually-Enhanced HPC codes (WAVE-HPC) for semiconductor R&D
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97 MATHEMATICS AND COMPUTING↗
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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.
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Some long, rate one-half, binary convolutional codes with an optimum distance profile and the systematic versus nonsystematic code question
A tabulation is given of long systematic and long quick-look-in (QLI) nonsystematic rate R = 1/2 binary convolutional codes with an optimum distance profile (ODP). These codes appear attractive for use with sequential decoders. Simulations for two of the new codes are reported and confirm Massey's conjecture that systematic and non-systematic codes of the same rate yield nearly identical computational and error probability performance with sequential decoding when the number of digits transmitted in the tail of the encoded frame is the same for both codes.
Johannesson, R.↗
A Simulator for Neyer Tests of Explosives
Explosives and explosive devices such as detonators are typically tested by applying a range of stimuli such as voltage or mechanical shock, and recording binary “detonated/did not detonate” responses. These are analyzed using maximum likelihood or generalized linear models to provide estimates of quantities such as the all-fire and no-fire points. Given that the true threshold for detonation is unknown a priori , sequential design methods are typically used to optimize the set of test points. One popular method, implemented in commercial software, is Neyer’s algorithm. To support simulation and experimental design, we have developed code in the R programming language to duplicate the functions of the Neyer software. We provide code for the simulator along with a description and examples of usage.
42 ENGINEERING↗
Real-time minimal bit error probability decoding of convolutional codes
A recursive procedure is derived for decoding of rate R=1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e. fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications such as in the inner coding system for concatenated coding.
Lee, L. N.↗
Real-time minimal-bit-error probability decoding of convolutional codes
A recursive procedure is derived for decoding of rate R = 1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit, subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e., fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications, such as in the inner coding system for concatenated coding.
Lee, L.-N.↗
CTT: Tools for Fine Alignment of Flash X-ray Systems
The CTT code is a compilation of the python code that was prototyped in the interest of making a method for fine alignment of Flash X-ray Systems at the lab. It contains python code for interacting with LTT and running optimization loops using LTT simulations or ray tracing with RaySpace. It Includes classes for creating phantom objects and modular geometry objects in the simulations. It allows one to generate a random phantom that has been optimized to stay with a certain cubic volume and maximize the minimum distance between any two ball phantom centers in all projections. It was primarily made to work on ball phantoms which were simulated as Teflon spheres. It allows the alignment from some nominal position to some displaced position to simulate recovery of a real geometry from the nominal geometry of the system. Fine alignment can be done with the projections in LTT while a rough alignment is faster using rayspace. If rayspace works well for the use case it should be preferred since it is considerably faster and less resource intensive in general. Some Notes about using this code is that one will have to edit the imports for the files to get to the correct LTT path, LTT GUI path and to the CTT path when importing. This was made by using anaconda with python 3 on windows 10. The LTT code was stored in a anaconda environment which seemed to help the python find the LTT although it shouldn’t be necessary if you append the path in your code using sys.path.append(r'add the path you want here’). The sys.path.append method is a quick way to give your python code access to a given folder when running it (such as LTT or CTT). Note that since the code was originally made with paths for a specific machine that a new user will have to edit those paths to make it work in all the files that use the old paths. This is somewhat tedious but will be required to run the code on a new machine. The methodology used to run and make these notebooks starts with opening a command prompt as administrator in windows 10. After this one would activate the anaconda environment in the appropriate directory using “conda activate myenv” in the command prompt. After this open a jupyter-notebook using the keyword “jupyter-notebook". After that a notebook should open in a browser. Note that some libraries used may not come with anaconda so those may have to be installed. There shouldn’t be much though since the main things used are scipy, numpy, matplotlib, and LTT. LTTQuicksetup also requires some paths that will be specific to the computer so that should be changed as well.
42 ENGINEERING↗
On the error probability of general tree and trellis codes with applications to sequential decoding
An upper bound on the average error probability for maximum-likelihood decoding of the ensemble of random binary tree codes is derived and shown to be independent of the length of the tree. An upper bound on the average error probability for maximum-likelihood decoding of the ensemble of random L-branch binary trellis codes of rate R = 1/n is derived which separates the effects of the tail length T and the memory length M of the code. It is shown that the bound is independent of the length L of the information sequence. This implication is investigated by computer simulations of sequential decoding utilizing the stack algorithm. These simulations confirm the implication and further suggest an empirical formula for the true undetected decoding error probability with sequential decoding.
Johannesson, R.↗
Preliminary Implementation of Two-Dimensional Cartesian Solver in CTF-R
Sub-channel codes are one of the the modeling and simulation tools used for thermal-hydraulic analysis of nuclear reactors. A few examples of such sub-channel codes are the COolant Boiling in Rod Arrays (COBRA) family of codes. The approximations that are used to simplify the fluid conservation equations into sub-channel form, mainly that of axially-dominated flow, lead to noticeable limitations on sub-channels solvers for problems with significant flow in lateral directions. In this report, a two-dimensional Cartesian solver is developed and implemented within CTF-R, which is the residual solver in the North Carolina State University version of COBRA-TF (CTF). The new solver will enable CTF to simulate flow that is not axially-dominated. The appropriate Cartesian forms of the conservation equations are derived and implemented in the solver. Once the conservation equations are established, the process of constructing the matrix system was altered to solve a two-dimensional staggered grid system. A simple case was used to test that the two-dimensional Cartesian solver is accurate. The test problem does not include any source terms or flow in the lateral direction. The results show that the solver was able to run the simple case and converge to a steady-state solution. Future work will focus on testing existing capabilities by using test cases that include transients and equation cross-terms. Future work will also include adding additional capabilities such as enabling the solver to include cases with source terms and three dimensional cases.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Overview 2003 of NASA Multi-D Stirling Convertor Code Development and DOE and NASA Stirling Regenerator R and D Efforts
This paper win report on continuation through the third year of a NASA grant for multi-dimensional Stirling CFD code development and validation; continuation through the third and final year of a Department of Energy, Golden Field Office (DOE), regenerator research effort and a NASA grant for continuation of the effort through two additional years; and a new NASA Research Award for design, microfabrication and testing of a "Next Generation Stirling Engine Regenerator." Cleveland State University (CSU) is the lead organization for all three efforts, with the University of Minnesota (UMN) and Gedeon Associates as subcontractors. The Stirling Technology Company and Sun power, Inc. acted as unfunded consultants or participants through the third years of both the NASA multi-D code development and DOE regenerator research efforts; they win both be subcontractors on the new regenerator microfabrication contract.
Tew, Roy↗
mrizwanriaz/lcm-dataset
Laser capture microdissection (LCM) derived stem cell-type transcriptome (Jie et al.) How to run on your system Install R on your system. Install the required packages shiny, shinyjs, ggplot2, dplyr, formattable, rcartocolor Download the RShiny app code (ui.R and server.R) and RDS files from the GitHub repository to the same directory. Usage: Run the R code file (ui.R) in the RStudio. The app will open in the default web browser.
Riaz, Muhammad Rizwan↗
Benchmarking of massively parallel phase-field codes for directional solidification
We present a detailed benchmark comparing two state-of-the-art phase-field implementations for simulating alloy solidification under experimentally relevant conditions. The study investigates the directional solidification of Al-3wt%Cu under high-velocity solidification conditions and SCN-0.46wt% camphor under microgravity conditions from National Aeronautics and Space Administration (NASA) DECLIC-DSI-R experiments. Both codes, one employing finite-difference discretization with uniform mesh and GPU-acceleration (GPU-PF) and the other one employing finite-element discretization with adaptive-mesh and CPU-parallelization (PRISMS-PF), solve the same quantitative phase-field formulation that incorporates an anti-trapping current for the solidification of dilute alloys. We evaluate the predictions of each code for dendritic morphology, primary spacing, and tip dynamics in both 2D and 3D, as well as their numerical convergence and computational performance. While existing benchmark problems have primarily focused on simplified or small-scale simulations, they do not reflect the computational and modeling challenges posed by employing experimentally relevant time and length scales. Our results provide a practical framework for assessing phase-field code performance as well as validating and facilitating their application in integrated computational materials engineering (ICME) workflows that require integration with realistic experimental data.
36 MATERIALS SCIENCE↗
Data for Grogan et al. "Bringing Hydrologic Realism to Water Markets"
This data set provides model output and post-processing files required to reproduce the results, tables, and figures in the paper "Bringing Hydrologic Realism to Water Markets" by Grogan et al. (in review). Other input data used in this study includes: Lisk, M., Grogan, D., Zuidema, S., Caccese, R., Peklak, D., Zheng, J., Fisher-Vanden, K., Lammers, R., Olmstead, S., & Fowler, L. (2023). Harmonized Database of Western U.S. Water Rights (HarDWR) (Version v1) [Data set]. MSD-LIVE Data Repository. https://doi.org/10.57931/2205619 Two models were used in this study: (1) The University of New Hampshire Water Balance Model WBM, and (2) a Water Market Model. Market model code and model output post-processing code that make use of these data can be found here Model output files are: 1. WBM output files: scenario[x]_wbm_output.zip Where [x] is one of 1, 2, 2a, 3, and 3a Each zipped directory contains 7 gridded NetCDF files, each reporting the 10-year annual average value of a given variable, in units of average mm/day: File Name: wbm_indUseGross_yc.nc; Description: Water withdrawals by industry (part of the urban sector) File Name: wbm_domUseGross_yc.nc; Description: Water withdrawals by the domestic sector (part of the urban sector) File Name: wbm_irrigationGross_yc.nc; Description: Water withdrawals for agriculture File Name: wbm_irrigationExtra_yc.nc; Description: Water withdrawals from unsustainable groundwater for agriculture File Name: wbm_indUseEvap_yc.nc; Description: Consumptive water use by industry File Name: wbm_domUseEvap_yc.nc; Description: Consumptive water use by the domestic sector File Name: wbm_irrigationNet_yc.nc; Description: Consumptive water use by agriculture The file full_cell_area.nc gives the area of each grid cell in km2, which is used for converting water depth to water volume. 2. Water market model output & post processing output Folder: marketTrdSummaries/ Description: Files in this folder are used as input to code 1_WelfareCalculation_actual_trades.R. They summarize historical water right trade transactions in each state. File Name: welfare_gain_by_state_sector.csv; Description: Welfare gains by state and sector, as shown in Figure 3F. Used in code Figure3.R and produced (as a .xlsx file) by code 2_DemandCurves_simulated_trades.R File Name: welfare_data_actual.rdata; Description: welfare gains by WMA from actual historical trades, as shown in Figure 3A. This data is the output of code 1_WelfareCalculation_actual_trades.R File Name: welfare_summary_simulated.xlsx; Description: Welfare gains by state as simulated by the market model in Scenario 1. Produced by code 2_DemandCurves_simulated_trades.R, and used in code 4_WelfareCalculation.R. File Name: welfare_summary_cutoffs.xlsx; Description: Welfare gains by state as simulated by the market model in Scenario 2. Produced by code 3_DemandCurves_simulated_trades_cutoffs.R, and used in code 4_WelfareCalculation.R. File Name: welfare_summary_cutoffs_SGMS.xlsx; Description: Welfare gains by state as simulated by the market model in Scenario 2a. Produced by code 3_DemandCurves_simulated_trades_cutoffs.R, and used in code 4_WelfareCalculation.R. File Name: welfare_data_actual.rdata; Description: Spatial data, actual historical welfare gains by WMA as shown in Figure 3A. Produced by code 4_WelfareCalculation.R and used by code Figure3.R. File Name: welfare_data_simulated.rdata; Description: Spatial data, simulated Scenario 1 welfare gains by WMA as shown in Figure 3B. Produced by code 4_WelfareCalculation.R and used by code Figure3.R. File Name: welfare_data_simulated_cutoffs.rdata; Description: Spatial data, simulated Scenario 2 welfare gains by WMA. Produced by code 4_WelfareCalculation.R and used by code Figure3.R. File Name: welfare_data_simulated_cutoffs_SGMA.rdata; Description: Spatial data, simulated Scenario 2a welfare gains by WMA. Produced by code 4_WelfareCalculation.R and used by code Figure3.R. Additional files are provided for efficient reproduction of tables and figures. These include: File Name: wma_thresold_dates_Scenario2(a).csv; Description: Wet vs. paper right threshold dates for each WMA. Shown in Figure 2A,B. Produced and used by code calculate_thresolds_Figure2.R File Name: WWRTradeBounds (directory); Description: Trade boundary shapefile required to reproduce Figure 3A-D. Used in code Figure3.R File Name: welfare_region_totals.csv; Description: Welfare gains for the entire study region, as shown in Figure 3E. Used in code Figure3.R File Name: Welfare_gain_by_state_sector.csv; Description: Welfare gains by state and sector, as shown in Figure 3F. Used in code Figure3.R and produced (as a .xlsx file) by code 2_DemandCurves_simulated_trades.R File Name: WECC_MERIT_5min_v3b_mask.nc; Description: Gridded file that identified which land grid cells are in the WBM model domain, used for processing in code Figure4.py File Name: Table_1.csv; Description: All data in Table 1, reproducible from WBM output files using code table_1.R
Economics↗
Validation of ray-based cross-beam energy transfer models
Ray-based cross-beam energy transfer (CBET) models have become a common feature of the radiation-hydrodynamic codes used to simulate inertial confinement fusion experiments. Here, these models are necessary for achieving better agreement with experimental measurements, but their detailed implementation can vary widely between the codes and often rely on artificial multipliers. To address this, a series of 2D and 3D test cases has been developed with validated solutions from wave-based calculations. Comparisons of various ray-based CBET models to the wave-based calculations highlight the essential physics that is required for accurate ray-based CBET modeling. Quantitative comparison metrics and/or field data from the wave-based calculations have been made available for use in the validation of other ray-based CBET codes.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Data from: “Bald Cypress (Taxodium distichum) Knees Are Methane Sources Controlled by Geomorphology, Climate, and Hydrologic Extremes”
This dataset is associated with the manuscript “Bald Cypress (Taxodium distichum) Knees Are Methane Sources Controlled by Geomorphology, Climate, and Hydrologic Extremes”. Bald cypress “knees” (aboveground woody roots) have been shown to contribute to wetland methane (CH4) efflux, with large variation within and between studies. To explain this variation, we investigated spatial (i.e., across knee surface, within sites, between sites) and temporal dynamics of CH4 fluxes from knees. Methane fluxes were collected from September 2022 to August 2024 at three locations in western Kentucky, USA, within the Mississippi Alluvial Valley: a main channel (semi-permanently flooded), side channel (seasonally flooded), and reservoir edge (artificially flooded). Knee CH4 fluxes (“Ross_et_al_Knee_Flux_Data.csv”) were measured from multiple heights on knees (20, 40, and 60 cm) of various sizes (knee straight height ranged from 24 to 93 cm) using a LiCOR LI-7810 CH4/CO2/H2O Trace Gas Analyzer. The dataset also includes environmental variables collected with each knee measurement, including water level adjusted for knee-to-knee elevational differences, subsurface and air temperature, and humidity. Soil CH4 fluxes (“Ross_et_al_Soil_Flux_Data.csv”) were also collected adjacent to knees (starting in April 2023) when water levels didn’t overtop soil collars, using a LiCOR Smart Chamber and calculated in SoilFluxPro software. The soil flux dataset includes associated variables collected by the Smart Chamber. Three separate files (“*_Water_Level.csv”) are included for water level and subsurface temperature data collected at each site using HOBO U20L barometric pressure loggers. Each file type (knee flux, soil flux, water level) has an associated data dictionary (“*_dd.csv”). For specifics on methodology used and calculations, see the associated manuscript. The R script includes code used for figures and analyses reported in the manuscript.
54 ENVIRONMENTAL SCIENCES↗
Errors in GPS due to Satellite C1-P1 Code Biases
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GPS Satellite C1-P1 Code Biases TurboRogue AOA Rog↗
A new 181 Ta neutron resolved resonance region evaluation
A new 181 Ta neutron resolved resonance region evaluation has been performed from the thermal energy range up to approximately 2.5 keV. The R-matrix SAMMY code was used with the Reich–Moore approximation to evaluate resonance parameters from several experimental data sets. A Monte Carlo approach was used for resonance spin assignments and generating 59 small fictitious resonance levels which were shown to improve the cumulative level, Porter-Thomas, and Wigner distributions as compared to theoretical predictions. Covariance information was also generated for the entire resolved resonance region. Finally, the positive impact of the new evaluation was validated through benchmark calculations which were sensitive to the 181 Ta cross section and showed improvement in the reactivity bias for several benchmark cases.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Local measurements of the spatial magnetic field distribution in a z-pinch plasma during and near stagnation using polarization spectroscopy
We present here the detailed measurements of radial distribution of the magnetic field in a gas-puff z-pinch plasma at the final stages of the implosion phase and at stagnation. While the measurements are chordal, the radial distribution of different charge states was utilized to measure the magnetic field locally for certain radii, so that unlike chordal measurements in general, the magnetic field radial distribution was obtained with no need for the Abel inversion of the data. The distribution was measured using the Zeeman effect via a novel spectroscopic technique, at several axial locations, and demonstrates striking features such as the peak field remaining at a radius much larger than the stagnation radius at all times. Furthermore, while the distribution observed is sometimes monotonic with respect to the radius, it is often not, a behavior that can be linked to 2D features in the plasma column resulting from the Rayleigh–Taylor instability. The current flowing through the stagnating plasma was found to be a small fraction of the total current, resulting in clearly insufficient magnetic pressure to balance the plasma pressure at stagnation. The magnetic field data, taken over several axial positions, are used to obtain the true inductance in the imploding plasma for the first time; it is found that the data cannot explain the current turnover at stagnation. A simulation with the MACH2-Tabular Collisional-Radiative Equilibrium magnetohydrodynamics code in the r–z plane shows that the peak of the magnetic field pinches to a much smaller radius than is observed in the spectroscopic data. Furthermore, the depth of the computed current turnover at stagnation is smaller than the measured one. The two observed features of a radially extended magnetic field at stagnation together with a deep current turnover are a challenge to match in simulations. Various calculations and estimates of the inductive and resistive load voltages are examined to ascertain if they are responsible for the observed current notch. Lastly, the results demonstrate that the knowledge of the true inductance in the driven load requires such magnetic-field-distribution measurements and that imaging data or electrical measurements are insufficient.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources
Abstract Motivation Precision medicine leverages patient-specific multimodal data to improve prevention, diagnosis, prognosis, and treatment of diseases. Advancing precision medicine requires the non-trivial integration of complex, heterogeneous, and potentially high-dimensional data sources, such as multi-omics and clinical data. In the literature, several approaches have been proposed to manage missing data, but are usually limited to the recovery of subsets of features for a subset of patients. A largely overlooked problem is the integration of multiple sources of data when one or more of them are completely missing for a subset of patients, a relatively common condition in clinical practice. Results We propose miss-Similarity Network Fusion (miss-SNF), a novel general-purpose data integration approach designed to manage completely missing data in the context of patient similarity networks. miss-SNF integrates incomplete unimodal patient similarity networks by leveraging a non-linear message-passing strategy borrowed from the SNF algorithm. miss-SNF is able to recover missing patient similarities and is “task agnostic”, in the sense that can integrate partial data for both unsupervised and supervised prediction tasks. Experimental analyses on nine cancer datasets from The Cancer Genome Atlas (TCGA) demonstrate that miss-SNF achieves state-of-the-art results in recovering similarities and in identifying patients subgroups enriched in clinically relevant variables and having differential survival. Moreover, amputation experiments show that miss-SNF supervised prediction of cancer clinical outcomes and Alzheimer’s disease diagnosis with completely missing data achieves results comparable to those obtained when all the data are available. Availability and implementation miss-SNF code, implemented in R, is available at https://github.com/AnacletoLAB/missSNF.
Biochemistry & Molecular Biology↗