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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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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
NASA NTRS2019

Microphone Phased Array NetCDF/HDF5 Archival Files: Application Program Interface Reference

An application program interface (API) has been developed for the creation and access of structured data files generated by microphone phased arrays utilized in aeroacoustics research. Two structured binary file formats are supported, namely NetCDF (Network Common Data Form) and HDF5 (Hierarchical Data Format) files. The API consists of a library of routines callable from C, Fortran or Matlab, with native versions of the API provided for each language. The libraries are divided into categories for file handling, file definition and initialization, data writing, data recovery, and error handling. The API is intended to provide a mechanism for generating self-describing binary files for long-term archiving of raw and processed data generated by phased array systems.

Humphreys, William M., Jr.↗
DOE OSTI2019

Systems and methods for generating slice files from native CAD geometries

A system and method for improving the production of objects with fully defined CAD models by generating CAD slice files from the native CAD geometries for use by AM machines. An electronic processing element receives the CAD model having a native and/or neutral format with metadata, determines a desired resolution, slices the CAD model to create the slice files having a slice format (e.g., point, edge, surface, volume) and retaining the metadata, and evaluates the slice files to determine whether the resolution has been achieved. If so, the slice files are sent to the AM machine. If not, a new desired resolution is determined and the CAD model is re-sliced, which may include combining the slice files to regenerate the CAD model. A support structure for the object may be analyzed, and if distortion is predicted, a modified CAD model may be created and sliced to create modified slice files.

Vernon, Gregory J.↗
DOE OSTI2016

FCP: A Fast and Scalable Data Copy Tool for High Performance Parallel File Systems

The design of HPC file and storage systems has largely been driven by the requirements on capability, reliability, and capacity. However, the convergence of large-scale simulations with big data analytics have put the data, its usability, and management back on the front and center position. One of the most common and time consuming data management tasks is the transfer of very large datasets within and across file systems.In this paper, we are introducing the FCP tool, a file system agnostic copy tool designed at the OLCF for scalable and high-performance data transfers between two file system endpoints. It provides an array of interesting features such as adaptive chunking, checksumming on the fly, checkpoint and resume capabilities to handle failures, and preserving stripe information for Lustre file system among others. It is currently available on the Titan supercomputer at the OLCF. Initial tests have shown that FCP has much better and scalable performance than traditional data copy tools and it was capable of transferring petabyte-scale datasets between two Lustre file systems.

Wang, Feiyi↗
DOE OSTI2022

Moving small files in a networked environment

Globally distributed computing infrastructures, such as clouds and supercomputers, are currently used to manage data that is generated with an unprecedented speed from a variety of resources. Coping with this trend, the volume of data exchanged across distant sites increases substantially. To accelerate data transfer, high-speed networks are provided to connect remote sites. Most existing data movement solutions are optimized for moving large files. However, it is still challenging to transfer a large number of small files across networks. This disadvantage not only lowers data transfer performance, but also decreases overall system utilization. Here, we identify that moving small files is mainly constrained by degraded file system throughput, not just network performance as might be suspected. We have built a data transfer pipeline model to analyze the impact of small network I/O and storage I/O on data movement. Extending one of the widely used open source data movement solutions, GridFTP, we demonstrate several appropriate engineering approaches that mitigate the bottleneck and increase data transfer efficiency. We show optimizations that improve data transfer performance more than 5 times. In comparison to existing solutions, our approaches can save a significant amount of system resources for moving lots of small files.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Redundancy Does Not Imply Fault Tolerance: Analysis of Distributed Storage Reactions to File-System Faults

In this paper, we analyze how modern distributed storage systems behave in the presence of file-system faults such as data corruption and read and write errors. We characterize eight popular distributed storage systems and uncover numerous problems related to file-system fault tolerance. We find that modern distributed systems do not consistently use redundancy to recover from file-system faults: a single file-system fault can cause catastrophic outcomes such as data loss, corruption, and unavailability. We also find that the above outcomes arise due to fundamental problems in file-system fault handling that are common across many systems. Finally, our results have implications for the design of next-generation fault-tolerant distributed and cloud storage systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

SparcleQC: Automated Input File Creation for QM/MM Studies of Protein:Ligand Complexes

SparcleQC is a Python package that, given a protein:ligand complex in the Protein Data Bank (PDB) file format, can create quantum mechanics/molecular mechanics (QM/MM)-like input files for the electronic structure theory packages PSI4, QChem, and NWChem. The resulting input files include quantum mechanical representations of the ligand and a small section of the protein, surrounded by point charges that represent the rest of the protein. Creation of these QM/MM input files includes cutting and capping the QM subregion, obtaining point charges for the protein, and adjusting charges at the QM/MM boundary; and each of these tasks are automated by the software. In this article, we describe the details of SparcleQC’s procedure, show examples of the Python API, and explain additional features that are helpful in protein:ligand interaction studies. Finally, we show that SparcleQC enables automated preparation of input files for QM/MM calculations, which can return can return accurate interaction energies in minutes, while a fully quantum mechanical computation on the protein:ligand complex could take days, if it is even possible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An Integrated Indexing and Search Service for Distributed File Systems

Data services such as search, discovery, and management in scalable distributed environments have traditionally been decoupled from the underlying file systems, and are often deployed using external databases and indexing services. However, modern data production rates, looming data movement costs, and the lack of metadata, entail revisiting the decoupled file system-data services design philosophy. In this article, we present TagIt, a scalable data management service framework aimed at scientific datasets, which can be integrated into prevalent distributed file system architectures. A key feature of TagIt is a scalable, distributed metadata indexing framework, which facilitates a flexible tagging capability to support data discovery. Furthermore, the tags can also be associated with an active operator, for pre-processing, filtering, or automatic metadata extraction, which we seamlessly offload to file servers in a load-aware fashion. We have integrated TagIt into two popular distributed file systems, i.e., GlusterFS and CephFS. Our evaluation demonstrates that TagIt can expedite data search operation by up to 10× over the extant decoupled approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

SU-E-T-576: Evaluation of Patient Specific VMAT QA Using Dynalog Files and Treatment Planning System

Purpose: This research investigates the use of Mult-ileaf Collimator (MLC) dynalog files to modify a Volumetric Arc Therapy (VMAT) DICOM Radiotherapy Treatment file from the Treatment Planning System (TPS) for quality assurance and treatment plan verification. Methods: Actual MLC positions and gantry angles where retrieved from the MLC Dynalog files of an approved and treated VMAT plan. The treatment machine used was a Novalis TX linac equipped with high definition MLC. The DICOM RT file of the plan was exported from the TPS (Eclipse, Varian Medical Systems) and the actual MLC leaf positions and gantry angles were inserted in place of the planned positions for each control point. The modified DICOM RT file was then imported back into the TPS where dose calculations were performed. The resulting dose distributions were then exported to VeriSoft (PTW) where a 3D gamma was calculated using 3mm-3% and 2mm-2% criteria. A 2D gamma was also calculated using dose measurements on the Delta4 (Sandidose) phantom. Results: A 3D gamma was calculated in Verisoft at 3mm-3% of 99.5% and at 2mm-2% of 99.2%. The pretreatment verification on the Delta4 yielded a 2D gamma at 3mm-3% of 97.9% and at 2mm-2% of 88.5%. The dose volume histograms of the approved plan and the dynalog plan are virtually identical. Conclusion: Initial results show good agreement of the dynalog dose distribution with the approved plan. Future work on this research will aim to increase the number of patients and replace the planned fractionated dose per control point with the actual fractionated dose.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2015

SU-E-T-784: Using MLC Log Files for Daily IMRT Delivery Verification

Purpose: To verify daily intensity modulated radiation therapy (IMRT) treatments using multi-leaf collimator (MLC) log files. Methods: The MLC log files from a NovalisTX Varian linear accelerator were used in this study. The MLC files were recorded daily for all patients undergoing IMRT or volumetric modulated arc therapy (VMAT). The first record of each patient was used as reference and all records for subsequent days were compared against the reference. An in house MATLAB software code was used for the comparisons. Each MLC log file was converted to a fluence map (FM) and a gamma index (γ) analysis was used for the evaluation of each daily delivery for every patient. The tolerance for the gamma index was set to 2% dose difference and 2mm distance to agreement while points with signal of 10% or lower of the maximum value were excluded from the comparisons. Results: The γ between each of the reference FMs and the consecutive daily fraction FMs had an average value of 99.1% (ranged from 98.2 to 100.0%). The FM images were reconstructed at various resolutions in order to study the effect of the resolution on the γ and at the same time reduce the time for processing the images. We found that the comparison of images with the highest resolution (768×1024) yielded on average a lower γ (99.1%) than the ones with low resolution (192×256) (γ 99.5%). Conclusion: We developed an in-house software that allows us to monitor the quality of daily IMRT and VMAT treatment deliveries using information from the MLC log files of the linear accelerator. The information can be analyzed and evaluated as early as after the completion of each daily treatment. Such tool can be valuable to assess the effect of MLC positioning on plan quality, especially in the context of adaptive radiotherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-233: Evaluation of Treatment Delivery Parameters Using High Resolution ELEKTA Log Files

Purpose: As modern linacs have become more technologically advanced with the implementation of IGRT and IMRT with HDMLCs, a requirement for more elaborate tracking techniques to monitor components’ integrity is paramount. ElektaLog files are generated every 40 milliseconds, which can be analyzed to track subtle changes and provide another aspect of quality assurance. This allows for constant monitoring of fraction consistency in addition to machine reliability. With this in mind, it was the aim of the study to evaluate if ElektaLog files can be utilized for linac consistency QA. Methods: ElektaLogs were reviewed for 16 IMRT patient plans with >16 fractions. Logs were analyzed by creating fluence maps from recorded values of MLC locations, jaw locations, and dose per unit time. Fluence maps were then utilized to calculate a 2D gamma index with a 2%–2mm criteria for each fraction. ElektaLogs were also used to analyze positional errors for MLC leaves and jaws, which were used to compute an overall error for the MLC banks, Y-jaws, and X-jaws by taking the root-meansquare value of the individual recorded errors during treatment. Additionally, beam on time was calculated using the number of ElektaLog file entries within the file. Results: The average 2D gamma for all 16 patient plans was found to be 98.0±2.0%. Recorded gamma index values showed an acceptable correlation between fractions. Average RMS values for MLC leaves and the jaws resulted in a leaf variation of roughly 0.3±0.08 mm and jaw variation of about 0.15±0.04 mm, both of which fall within clinical tolerances. Conclusion: The use of ElektaLog files for day-to-day evaluation of linac integrity and patient QA can be utilized to allow for reliable analysis of system accuracy and performance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-295: MLCs Performance and Patient-Specific IMRT QA Using Log File Analysis

Purpose: To analyze the performance of the multi-leaf collimators (MLCs) from the log files recorded during the intensity modulated radiotherapy (IMRT) treatment and to construct the relative fluence maps and do the gamma analysis to compare the planned and executed MLCs movement. Methods: We developed a program to extract and analyze the data from dynamic log files (dynalog files) generated from sliding window IMRT delivery treatments. The program extracts the planned and executed (actual or delivered) MLCs movement, calculates and compares the relative planned and executed fluences. The fluence maps were used to perform the gamma analysis (with 3% dose difference and 3 mm distance to agreement) for 3 IMR patients. We compared our gamma analysis results with those obtained from portal dose image prediction (PDIP) algorithm performed using the EPID. Results: For 3 different IMRT patient treatments, the maximum difference between the planned and the executed MCLs positions was 1.2 mm. The gamma analysis results of the planned and delivered fluences were in good agreement with the gamma analysis from portal dosimetry. The maximum difference for number of pixels passing the gamma criteria (3%/3mm) was 0.19% with respect to portal dosimetry results. Conclusion: MLC log files can be used to verify the performance of the MLCs. Patientspecific IMRT QA based on MLC movement log files gives similar results to EPID dosimetry results. This promising method for patient-specific IMRT QA is fast, does not require dose measurements in a phantom, can be done before the treatment and for every fraction, and significantly reduces the IMRT workload. The author would like to thank King Fahd University of petroleum and Minerals for the support.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Simulation Dataset - Input files

The input data that are required to run the model are divided into fundamental data and advanced data. The fundamental data are essential to run the model, while the advanced data allow optional model features to be activated. The names of all input data files are to be entered as ASCII characters in a tabular format. Spaces, commas, or tabs can separate numeric fields, the use of any other special visible or hidden characters must be avoided. It may be useful to note that all files are generally read in using standard free-format style FORTRAN READ statements. The input data files can be generated/modified using any standard editor, spreadsheet or word processor (in non-document mode), given that the above guidelines are complied with. However, the inclusion of special formatting characters and the insertion of blank lines must be avoided. The input data files may also be generated through the use of special purpose translation programs that convert the input data files that were initially generated for another traffic simulation or transportation planning model into an INTEGRATION format.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2018

Flexible File Sort Utility

This program sorts a text file alphabetically (forward or reverse). It supports both in-memory sorts for smaller files and use of temporary swap files for large files. It can alternatively sort on a column in a tab-delimited or comma-separated file. The column sort mode also supports numeric sorting.

Monroe, Matthew↗
DOE OSTI2024

Laboratory Upgrade Point Absorber (LUPA) CAD Files

The Laboratory Upgrade Point Absorber (LUPA) is an open-source wave energy converter designed and tested by Oregon State University. The computer-aided design (CAD) files are provided here in two forms: the original SOLIDWORKS (2021) model as "LUPA SOLIDWORKS.zip" and as a STEP file "LUPA-A1000.step". The bill of materials is provided as an Excel file with assemblies (LUPA-Axxx), part numbers (LUPA-Axxx-Pyyy), part descriptions, manufacturers, and manufacturer part numbers. This comprehensive CAD model represents LUPA as it was deployed in Fall 2022 testing at the O.H. Hinsdale Wave Research Laboratory. The mass properties including mass, center of gravity, and moments of inertia have been overridden for some parts and assemblies to match the physical device properties as determined from experiments. This appears as "overridden by user" when viewing mass properties in SOLIDWORKS. The LUPA-A1000.SLDASM file from the LUPA SOLIDWORKS.zip folder is the topmost assembly, open this file to see the entire model as one assembly. See "PMEC Page", "OpenEI Wiki Page", and the "Signature Project Page" resources below for more information on LUPA.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

Data-model files associated with the manuscript "The Effects of Spatial and Temporal Resolution of Gridded Meteorological Forcing on Watershed Hydrological Responses" (Shuai et al., 2022 HESS)

This data package contains the model inputs and outputs used in "The Effects of Spatial and Temporal Resolution of Gridded Meteorological Forcing on Watershed Hydrological Responses" (Shuai et al., 2022 HESS). The data.zip file contains the data used to drive the model simulations. The model.zip file contains the XML input file for ATS. The notebook.zip file contains the Jupyter notebooks for pre- and post- processing model results. The figures.zip file contains the raw figures associated with the manuscript.Meteorological forcing plays a critical role in accurately simulating the watershed hydrological cycle. With the advancement of high-performance computing and the development of integrated watershed models, simulating the watershed hydrological cycle at high temporal (hourly to daily) and spatial resolution (10s of meters) has become efficient and computationally affordable. These hyperresolution watershed models require high resolution of meteorological forcing as model input to ensure the fidelity and accuracy of simulated responses. In this study, we utilized the Advanced Terrestrial Simulator (ATS), an integrated watershed model, to simulate surface and subsurface flow and land surface processes using unstructured meshes at the Coal Creek Watershed near Crested Butte (Colorado). We compared simulated watershed hydrologic responses including streamflow, and distributed variables such as evapotranspiration, snow water equivalent (SWE), and groundwater table driven by three publicly available, gridded meteorological forcings (GMFs) -- Daily Surface Weather and Climatological Summaries (Daymet), Parameter-elevation Regressions on Independent Slopes Model (PRISM), and North American Land Data Assimilation System (NLDAS). By comparing various spatial resolutions (ranging from 400 m to 4 km) of PRISM, the simulated streamflow only becomes marginally worse when spatial resolution of meteorological forcing is coarsened to 4 km (or 30% of the watershed area). However, the 4 km resolution has much worse performance than finer resolution in spatially distributed variables such as SWE. Using temporally disaggregated PRISM, we compared models forced by different temporal resolutions (hourly to daily), sub-daily resolution preserves the dynamic watershed responses (e.g., diurnal fluctuation of streamflow) that are absent in results forced by daily resolution. Conversely, the simulated streamflow shows better performance using daily resolution compared to that using sub-daily resolution. Our findings suggest that the choice of GMF and its spatiotemporal resolution depends on the quantity of interest and its spatial and temporal scale, which may have important implications on model calibration and watershed management decisions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

ParFlow-CLM model simulation files for Maina et al., Journal of Hydrology, 2022

This dataset contains the files to run a ParFlow-CLM integrated hydrologic model simulation for Maina et al., HESS, 2022. It also contains the associated daily pressure output of those simulations. Simulations are for a hillslope-similarity approach based on seasonal groundwater changes in the East River, Colorado. Comparisons are made to different clustering, or functional zonation approaches. We assess the ability of these clustering approaches to identify and categorize hillslopes with similar static characteristics, hydroclimate, land surface processes, and subsurface dynamics in a mountainous watershed. ParFlow binary files (.pfb) are model specific, and can be modified/viewed with conversion to .sa, .silo, or .vtk file formats. ParFlow input scripts are in the .tcl file format. Associated post-processing scripts are included as .f90 files.

54 ENVIRONMENTAL SCIENCES↗