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DOE OSTI2024

ThunderBoltz API

The ThunderBoltz application programming interface (API) code is written in Python and is comprised of a set of tools to facilitate compilation of the ThunderBoltz code, as well as fast assembly and formatting of input files for the ThunderBoltz code, post-processing tools of ThunderBoltz results, plotting tools, and runs/schedules the ThunderBoltz code executable for calculations. The ThunderBoltz API code is utilized for importing and manipulating input cross section sets, input conditions, and any other simulation settings made available within the ThunderBoltz input deck via user-defined settings or via automatic generation. The API comes with a set of plotting capabilities of input cross sections, results from ThunderBoltz, and post-processed results carried out with the API.

Park, Ryan↗

DOE OSTI2022

Psychrometric Chart v1.0.0

Psychart is a graphical program developed for NERSC for accurately monitoring air conditions for the air cooled HPC equipment. Psychart will live directly in the OMNI system as a Grafana plugin. It employs the use of Psychrolib and the Grafana Starter Panel to create a front-end program that plots the state of the environmental air on a psychrometric chart. It is highly customizable, allowing the user to modify graph bounds, optionally show ASHRAE data center comfort regions, change the series point color, and more. What sets Psychart apart from other existing psychrometric charts is its ability to plot in real-time. Other psychrometric charts that can be found online require manual input of data and do not seamlessly integrate with Grafana.

Ventura, Nicolas↗

DOE OSTI2025

ggtaxplot v 0.0.1

ggtaxplot is an R package designed to process and visualize taxonomic data through a taxonomic river plot. This package is ideal for researchers and data scientists who need to visualize taxonomic data. ggtaxplot function processes data and generates a taxonomic river plot, allowing users to visualize the distribution of taxa across different samples.

Coclet, Clement [Lawrence Berkeley National Labora↗

DOE OSTI2026

Pumpchart v1.0.0

Pumpchart is a graphical tool that plots the state of a hydraulic system overlayed on a pump curve and system curve. It assists with determining the optimal performance of the system. One advantage of Pumpchart over other softwares is that it is integrated with the Grafana dashboarding software, so that data can be plotted in real-time for instant operator feedback. It is intended to be used at NERSC to monitor the performance of our cooling water pumps.

Venture, Nicholas [Lawrence Berkeley National Labo↗

DOE OSTI2026

GAT (Grid Analysis Toolkit) [SWR-25-41]

Grid Analysis Toolkit (GAT) is a unified Python API and plotting for power system PCM and CEM results (Sienna, PLEXOS, ReEDS™). It's a toolkit for wrangling data for Bulk Grid Dispatch and Transmission Analysis. GAT aims to provide simplified access to PCM and CEM results in a standard format while also allowing raw data access to underlying datasets specific to the model. This software can also be found on PyPI at For plotting, GAT defaults to standard National Lab of the Rockies (NLR) color schemes and standard styles while allowing customization.

Webb, Micah [National Laboratory of the Rockies (N↗

DOE OSTI2016

Spatial Mapping of Pyocyanin in Pseudomonas Aeruginosa Bacterial Communities Using Surface Enhanced Raman Scattering

Surface enhanced Raman spectroscopy (SERS) imaging was used in conjunction with principal component analysis (PCA) for the in situ spatiotemporal mapping of the virulence factor pyocyanin in communities of the pathogenic bacterium Pseudomonas aeruginosa. The combination of SERS imaging and PCA analysis provides a robust method for the characterization of heterogeneous biological systems while circumventing issues associated with interference from sample autofluorescence and low reproducibility of SERS signals. The production of pyocyanin is found to depend both on the growth carbon source and on the specific strain of P. aeruginosa studied. A cystic fibrosis lung isolate strain of P. aeruginosa synthesizes and secretes pyocyanin when grown with glucose and glutamate, while the laboratory strain exhibits detectable production of pyocyanin only when grown with glutamate as the source of carbon. Pyocyanin production in the laboratory strain grown with glucose was below the limit of detection of SERS. In addition, the combination of SERS imaging and PCA can elucidate subtle differences in the molecular composition of biofilms. As a result, PCA loading plots from the clinical isolate exhibit features corresponding to vibrational bands of carbohydrates, which represent the mucoid biofilm matrix specific to that isolate, features that are not seen in the PCA loading plots of the laboratory strain.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Secondary Crash Identification using Crowdsourced Waze User Reports

Secondary crashes are crashes that occur as a result of the nonrecurrent congestion originating from primary crashes, and always have a greater impact on safety and traffic than a single crash. A better understanding of secondary crashes would benefit traffic incident management, and this requires accurate identification of secondary crashes. This study explores using crowdsourced Waze user reports to identify secondary crashes. Here, a network-based clustering algorithm is proposed to extract the primary crash cluster, including all user reports originating from the primary crash, and any crash that occurred within the cluster would be a secondary crash. This method works as a filter to select accurate primary–secondary relationships, thus precisely identifying secondary crashes. A case study is performed with crashes occurring from June to December 2019 on a 30-mi stretch of I-40 in Knoxville, TN. A static threshold method (crash duration and 10 mi) was used to preselect the potential primary–secondary crash pairs, and 75 out of 708 crashes were identified as potential secondary crashes. Based on the preselected primary–secondary crash pairs, 17 secondary crashes were obtained with the proposed method and the results were compared with one of the commonly used methods, the speed contour plot method. Though the proposed method captured fewer secondary crashes, it did identify several secondary crashes that could not be observed with the speed contour plot method. The results showed the applicability of the method and the potential of crowdsourced Waze user reports in secondary crash identification.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2015

Elviz – exploration of metagenome assemblies with an interactive visualization tool

Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, including both the sequences themselves and metadata describing their abundance, assembly, predicted functional characteristics and environmental parameters. The ability to explore these data visually is critically important to meaningful biological interpretation. Current genomics applications cannot effectively integrate sequence data, assembly metadata, and annotation to support both genome and community-level inquiry. Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing. Compared to the current alternative of generating a succession of static figures, Elviz can greatly accelerate the speed of metagenome analysis. Elviz can be used to explore both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genome Institute (JGI). Elviz is freely available at http://genome.jgi.doe.gov/viz and runs on most current web-browsers.

59 BASIC BIOLOGICAL SCIENCES↗

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 OSTI2023

SoyFACE Fumigation Data Files

This data set is related to the SoyFACE experiments, which are open-air agricultural climate change experiments that have been conducted since 2001. The fumigation experiments take place at the SoyFACE farm and facility in Champaign County, Illinois during the growing season of each year, typically between June and October. - The "SoyFACE Plot Information 2001 to 2021" file contains information about each year of the SoyFACE experiments, including the fumigation treatment type (CO2, O3, or a combination treatment), the crop species, the plots (also referred to as 'rings' and labeled with numbers between 2 and 31) used in each experiment, important experiment dates, and the target concentration levels or 'setpoints' for CO2 and O3 in each experiment. - This data set includes files with minute readings of the fumigation levels ( "SoyFACE 1-Minute Fumigation Data Files" folder) from the SoyFACE experiments. The "Soyface 1-Minute Fumigation Data Files" folder contains sub-folders for each year of the experiments, each of which contains sub-folders for each ring used in that year's experiments. This data set also includes hourly data files for the fumigation experiments ( "SoyFACE Hourly Fumigation Data Files" folder) created from the 1-minute files, and hourly ambient/weather data files for each year of the experiments ( "Hourly Weather and Ambient Data Files" folder). The ambient CO2 and O3 data are collected at SoyFACE, and the weather data are collected from the SURFRAD and WARM weather stations located near the SoyFACE farm. - The "Fumigation Target Percentages" file shows how much of the time the CO2 and O3 fumigation levels are within a 10 or 20 percent margin of the target levels when the fumigation system is turned on. - The "Matlab Files" folder contains custom code (Aspray, E.K.) that was used to clean the "SoyFACE 1-Minute Fumigation Data" files and to generate the "SoyFACE Hourly Fumigation Data" and "Fumigation Target Percentages" files. Code information can be found in the "SoyFACE Hourly Fumigation Data Explanation" file. - Finally, the " * Explanation" files contain information about the column names, units of measurement, and other pertinent information for each data file. * NOTE: We have identified some files in the “SoyFACE 1-Minute Fumigation Data Files” folder in our SoyFACE data set submission that were not downloaded properly - the files were present in the folder, but the actual files were empty. V3 ensures that there are no longer any empty files in the data set.

agricultural↗

DOE OSTI2026

Data for "Plasmon-driven exciton formation in a non-equilibrium Fermi liquid"

This repository contains source data for key plots presented in the manuscript "Plasmon-driven exciton formation in a non-equilibrium Fermi liquid." Experimental data that was analyzed in Igor Pro 8 are presented as the .pxp files used to generate individual sub-plots. Electronic spectral function calculations are provided as .txt files, in which consecutive rows refer to the meshgrid x coordinate, y coordinate, spectral function (and, where relevant, axis-projected local angular momentum). We additionally include the Wannier model and DFT-obtained bulk band structure on which the Wannier model was based. Files are named as the number of the figure in the manuscript to which they correspond, with additional details included where necessary. Details of file names: 2a_DOS_Lxz_Ek_KGM_40layer_xnum_800kpt_tot.txt: Density of states, xz-axis projected local orbital angular momentum, for 800 points along the K-Gamma-M path, for a 40-layer model. 2c_composite_y.pxp: ARPES (angle-resolved photoemission spectroscopy) spectra along the ky axis, including both a scan near the Fermi level and a scan at high kinetic energies. 2d_LCP_RCP_diff_Sect_20K.pxp: difference between ARPES constant energy cuts at T=20 K at E0 + 0.23 eV taken with left- and right-circularly polarized photons. The polarization-integrated intensity at the constant energy cut is also included. 2e_DOS_L45_E11pt79_m0pt25to0pt25_xnum_800kpt_tot.txt: Density of states, xz-projected local orbital angular momentum, and corresponding k-points in two dimensions from ab-initio electronic structure calculations for a constant-energy cut. 3a_[x]_[y]ps: ARPES cut under excitation at a fluence of x uJ/cm2, measured y ps after photoexcitation. Measurements were performed at 9 K. 3b_[x]: Energy distribution curves under excitation at a fluence x uJ/cm2 at selected delay times after photoexcitation. 4a_ImSigma_vs_temperature.pxp: Imaginary self energy (extracted from ARPES linewidths) at different energies above E0 for selected lattice temperatures. 4b_EELS_lowE.pxp: Electron energy loss spectrum over a low energy range 5b_diff_55m15.pxp: Difference between momentum-integrated Tr-ARPES traces at 55 uJ/cm2 and 15 uJ/cm2 photoexcitation. Time-dependent intensity at each energy level has been normalized to a maximum of 1 for each individual fluence prior to subtraction. 5d_invtau_at_EX_vs_fluence.pxp: decay rate at a specified energy EX for different excitation fluences, from single exponential fits. NOTE: Analyses based on the Wannier model presented here should cite both the associated Article and this dataset. For all other files in the repository, citing the dataset alone is sufficient.

Acharya, Rishi [University of Illinois] (ORCID:000↗

DOE OSTI2026

Two-stage formation-energy correction (NbZr, TaZr, VZr)

This bundle contains the scripts, the raw and corrected per-structure data, and the manuscript plots for the NbZr / TaZr / VZr BCC binary formation energies and the associated RMSDs. Why a two-stage correction is necessary: The "raw" formation energy of every relaxed VASP configuration is computed in the usual way, FE_raw(c) = E_alloy(c) - sum_i x_i * E_pure_i , where E_pure_i are the per-atom total energies of the pure-element reference structures (Nb, Ta, V, Zr in the same BCC supercell, with identical INCAR / KPOINTS / PAW choices). With perfectly consistent reference runs the raw FE should vanish at the two pure-element endpoints (x = 0 and x = 1) by construction. In practice this does not hold for two reasons that are present in our dataset: 1. Reference-energy inconsistency (composition-dependent bias). Even with identical input parameters, the pure-element runs (stored in `corrected_DFT_pure_element_runs/`) differ slightly from the values that would be implied by the alloy runs at near-pure compositions (a few meV/atom). This bias is approximately linear in concentration, because the residual error in E_pure_Nb (or E_pure_Ta / E_pure_V) propagates into FE_raw(c) as (1 - x) * dE_pure_1, and the corresponding error in E_pure_Zr propagates as x * dE_pure_2. Left uncorrected, this produces a non-physical "tilt" of FE_raw(x) and shifts the entire FE-vs-x cloud away from zero at the endpoints. 2. Endpoint anchoring against the audited true endpoints. The strict endpoint values (FE_x0_meVatom, FE_x1_meVatom in `corrected_fe_strict_endpoints_20260518/strict_endpoint_check_20260518.csv`) were re-derived from an independent cross-check of the pure-element runs. After stage 1 removes the linear bias, the near-pure compositions in the alloy dataset still extrapolate to values that differ slightly from these audited endpoints — because stage 1 is fit from a few near-end alloy bins, not from the audited pure-element references themselves. The README.txt file discusses how these issues are addressed by the two-stage correction, and describes folder layout, pipeline summary, and how to re-run.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Visualizing spatiotemporal pulse propagation: first-order spatiotemporal couplings in laser pulses

Even though a general theory of first-order spatiotemporal couplings exists in the literature, it is often difficult to visualize how these distortions affect laser pulses. In particular, it is difficult to show the spatiotemporal phase of pulses in a meaningful way. We propose a general solution to plotting the electric fields of pulses in three-dimensional space that intuitively shows the effects of spatiotemporal phases. The temporal phase information is color-coded using spectrograms and color response functions, and the beam is propagated to show the spatial phase evolution. In using this plotting technique, we generate two- and three-dimensional images and movies that show the effects of spatiotemporal couplings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2014

Bouncing Back: Plant-Associated Soil Microbes Respond Rapidly to Prairie Establishment

It is well established that soil microbial communities change in response to altered land use and land cover, but less is known about the timing of these changes. Understanding temporal patterns in recovering microbial communities is an important part of improving how we assess and manage reconstructed ecosystems. We assessed patterns of community-level microbial diversity and abundance in corn and prairie plots 2 to 4 years after establishment in agricultural fields, using phospholipid fatty acid biomarkers. Principal components analysis of the lipid biomarkers revealed differing composition between corn and prairie soil microbial communities. Despite no changes to the biomass of Gram-positive bacteria and actinomycetes, total biomass, arbuscular mycorrhizal fungi biomass, and Gram-negative bacteria biomass were significantly higher in restored prairie plots, approaching levels found in long-established prairies. These results indicate that plant-associated soil microbes in agricultural soils can shift in less than 2 years after establishment of perennial grasslands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Microclimatic performance of a free-air warming and CO₂ enrichment experiment in windy Wyoming, USA

In order to plan for global changing climate experiments are being conducted in many countries, but few have monitored the effects of the climate change treatments (warming, elevated CO₂) on the experimental plot microclimate. During three years of an eight year study with year-round feedback-controlled infra-red heater warming (1.5/3.0°C day/night) and growing season free-air CO₂ enrichment (600 ppm) in the mixed-grass prairie of Wyoming, USA, we monitored soil, leaf, canopy-air, above-canopy-air temperatures and relative humidity of control and treated experimental plots and evaluated ecologically important temperature differentials. Leaves were warmed somewhat less than the target settings (1.1 & 1.5°C day/night) but soil was warmed more creating an average that matched the target settings extremely well both during the day and night plus the summer and winter. The site typically has about 50% bare or litter covered soil, therefore soil heat transfer is more critical than in dense canopy ecosystems. The Wyoming site commonly has strong winds (5 ms⁻¹ average) and significant daily and seasonal temperature fluctuations (as much as 30°C daily) but the warming system was nearly always able to maintain the set temperatures regardless of abiotic variation. The within canopy-air was only slightly warmed and above canopy-air was not warmed by the system, therefore convective warming was minor. Elevated CO₂ had no direct effect nor interaction with the warming treatment on microclimate. Relative humidity within the plant canopy was only slightly reduced by warming. Soil water content was reduced by warming but increased by elevated CO₂. This study demonstrates the importance of monitoring the microclimate in manipulative field global change experiments so that critical physiological and ecological conclusions can be determined. Highly variable energy demand fluctuations showed that passive IR heater warming systems will not maintain desired warming for much of the time.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Utah FORGE: GIS Well Temperature Data

This is a GIS point feature shapefile representing wells, and their temperatures, that are located in the general Utah FORGE area near Milford, Utah. There are also fields that represent interpolated temperature values at depths of 200 m, 1000 m, 2000 m, 3000 m, and 4000 m. in degrees Fahrenheit. The temperature values at specific depths as mentioned above were derived as follows. In cases where the well reached a given depth (200 m and 1, 2, 3, or 4 km), the temperature is the measured temperature. For the shallower wells (and at deeper depths in the wells reaching one or more of the target depths), temperatures were extrapolated from the temperature-depth profiles that appeared to have stable (re-equilibrated after drilling) and linear profiles within the conductive regime (i.e. below the water table or other convective influences such as shallow hydrothermal outflow from the Roosevelt Hydrothermal System). Measured temperatures/gradients from deeper wells (when available and reasonably close to a given well) were used to help constrain the extrapolation to greater depths. Most of the field names in the attribute table are intuitive, however HF = heat flow, intercept = the temperature at the surface (x-axis of the temperature-depth plots) based on the linear segment of the plot that was used to extrapolate the temperature profiles to greater depths, and depth_m is the total well depth. This information is also present in the shapefile metadata.

15 GEOTHERMAL ENERGY↗

DOE OSTI2022

Mass of Water Turbine Current Energy Converter CFD Results

The CFD (computational fluid dynamics) results for the Mass of Water Turbine (MOWT) current energy converter from MWNW Consulting (formerly Ecosse IP). Each case is self-contained in its own tar.gz archive file. The archive contains the scripts required to perform a full simulation using OpenFOAM v1906. The scripts to process the output and plot forces are included in "Plotting Scripts", and all computational meshes generated are included in "Computational Grids".

16 TIDAL AND WAVE POWER↗

DOE OSTI2018

FACE-MDS Phase 2: Data from Six US-Located Elevated CO2 Experiments

This dataset contains measured ecosystem data from four Free Air CO2 Enrichment (FACE) experiments–Duke, Oak Ridge (ORNL), and Rhinelander -- and one Open Top Chamber (OTC) experiment -- Kennedy Space Center (KSCO). The sites were located in the United States and contain data from 1996-2009. These sites were the study sites of the FACE Model Data Synthesis (FACE-MDS) project phase 2. The file naming convention can be found in the file 'facemds-file-table-sitedata.xml' and information about variable naming convention can be found in the file 'facemds-standard-name-table-modvars.xml'. We followed the ALMA v3 convention for meteorological variables and developed a hierarchical naming scheme for ecosystem variables. Additional info can be found in the protocols in the accompanying meteorological dataset (Walker et al. 2018: doi:10.15485/1480328). We replaced the original naming convention mentioned in the protocol with the one described in 'facemds-standard-name-table-modvars.xml'. The outputs of the FACE-MDS phase 2 are in Walker et al (2018: doi:10.15485/1480327). The dataset contains 18 data files that are available in comma-separate (*.csv), and 18 R Data Serialization (*.rds) format. 2 XML (*.xml) companion files and additional metadata are provided: 2 data dictionaries and a file-level metadata file in comma-separate (.csv) format and a user guide in PDF (*.pdf) format. This dataset was updated on 2019-06-28 to fix daily files at Duke and ORNL were incorrectly labelled and were standard error files instead of plot level data. Now corrected and all three (plot, mean, standard error) daily data files for both sites have been added. This dataset was updated on 2026-06-08 to add a user guide, data dictionary file, and a file-level metadata file. DUKE_ax_v2.csv was added to match the no data value format of other files in this dataset. DUKE_ax.csv is maintained as a data file. No previously released data values were changed.

54 ENVIRONMENTAL SCIENCES↗