AndreaBozzo/ceres-open-data-index huggingface dataset:
An example data set to demonstrate the usage of M.o.R., a shiny app for model-based metrology.

This data set consists of several files that were created to accompany M.o.R., a shiny app created by the Surface & Nanostructure Metrology Group in the Engineering Physics Division of the Physical Measurement Laboratory (PML) at the National Institute of Standards and Technology. It was created to simplify model-based metrology. A detailed explanation of the proper usage can be found in the M.o.R. documentation.

Tags: model-based-metrology, statistics
Organization: National Institute of Standards and Technology
NISTfit

NISTFIT is a heavily abstracted C++-based kernel for fitting correlations. The software is written in our source languages. The current trend in computer architecture is for increasingly parallel computation while the clock frequency stagnates. The increase in computing speed is achieved by dividing a process into several threads which are executed in parallel on multiple processors, processors with multiple cores, cores that are able to handle multiple threads (hyper-threading), graphical processing units (GPU), or co-processors. In order to take advantage of these new architectures, algorithms that have historically been implemented for serial evaluation need to be refactored for parallelization. In this work, a native multithreading framework in C++11 for scientific and engineering model development is presented. The motivation for NISTfit is to develop a modern C++11-based library for this problem that is: ?          Cross-platform: NISTfit has only very minimal header-only dependencies (Eigen and ThreadPool), and builds reliably on all major architectures; a CMake build file is provided. ?          Easy to use: There are a multitude of similar libraries for model fitting (e.g., MINPACK 1, levmar2, Eigen?s Levenberg-Marquardt module 3, to name but a few) that a) are based on archaic FORTRAN/C/C++ constructs, b) require significant boilerplate to solve simple problems, or c) have difficult-to-build dependencies. It is the opinion of the authors of NISTfit that NISTfit strikes a good balance of power and ease-of-use for simple fitting problems. The code utilizes modern C++11 constructs and will build on any C++11 compliant compiler. ?          Parallelizable: The future is parallel, and NISTfit is able to achieve near theoretical speedup as more cores are made available to the fitting for sufficiently expensive models.

Tags: model-fitting, optimization, thermodynamics
Organization: National Institute of Standards and Technology
Cloud of Reproducible Records

Cloud of Reproducible Records (CoRR) is a web platform to support computation version control tools such as Sumatra, Reprozip, CDE, and NoWorkflow. These tools are seen as support for reproducible research, yet they are facing issues in adoption when compared to their source code counterparts like Git, Subversion, and Mercurial. This is mostly due to the fact that the latter have support from web platforms dedicated to increasing their content exposure, i.e. Github, Bitbucket, SourceForge, etc.  CoRR is a scientific social network around reproducible records dedicated to helping increase their adoption by boosting exposure of the records.  The platform focuses on networking records and scientists, which makes the long-term survival of research reproducibility its core goal.

Tags: computation, corr, platform, reproducible, version-control, web
Organization: National Institute of Standards and Technology
CT data for "Intrinsic dimensionality of Hounsfield unit measurements: Implications for a link to the SI"

Data will be posted here to allow re-analysis of published work.  Typical CT data sets are up to 1 gigabyte in size.  Medical CT yields data in DICOM format.

Tags: x-ray-computed-tomography-medical-phantom-hounsfield-unit-volume-shape
Organization: National Institute of Standards and Technology
CHiMaD Phase Field

CHiMaD Phase Field - Integrating the phase field community



In January 2015 a group of phase field theorists and code developers met at Northwestern University to discuss ways for the community to improve code collaboration efforts. Everyone agreed that the community needs to become more open and work in a more collaborative manner.

A key factor to improving community code collaboration is to develop resources to compare and contrast phase field codes and libraries. This site aims to provide some of these resources and become a useful web service for phase field practitioners.


Tags: jekyll-website, materials-science, phase-field
Organization: National Institute of Standards and Technology
FEASST: Free Energy and Advanced Sampling Simulation Toolkit

The Free Energy and Advanced Sampling Simulation Toolkit (FEASST) is a free, open-source, modular program to conduct molecular and particle-based simulations with flat-histogram Monte Carlo and molecular dynamics methods. It is a software written in C++ and python which is made publicly available to aid in reproducibility. It is also provided as a service to the scientific community in which there are few , if any, Monte Carlo programs that support flat histogram methods and advanced sampling algorithms. This software is expected to be updated frequently with new methods.

Tags: c_, flat-histogram, free-energy, molecular-simulation, monte-carlo, python
Organization: National Institute of Standards and Technology
DFT Benchmarking

All the data in this project are generated running Density Functional (DFT) simulation either on NIST computer clusters of through our collaborators at University of Florida. The final data consist in relaxed atomic structures and corresponding energetic, mechanical, electronic and phonon properties. The metadata consist in the initial and relaxed structures, the description of the code, of the k points and of all the parameters used in running the simulations (energy or real space cutoff, type of minimization, occupation, etc.).

Tags: bulk-modulus, density-functional-theory, dft, elastic-constants, energy, energy-gap, energy-precision, exchange-correlation-comparison, k-points, uncertainty, uq
Organization: National Institute of Standards and Technology
JARVIS: Joint Automated Repository for Various Integrated Simulations

JARVIS (Joint Automated Repository for Various Integrated Simulations) is a repository designed to automate materials discovery using classical force-field, density functional theory, machine learning calculations and experiments.

The Force-field section of JARVIS (JARVIS-FF) consists of thousands of automated LAMMPS based force-field calculations on DFT geometries. Some of the properties included in JARVIS-FF are energetics, elastic constants, surface energies, defect formations energies and phonon frequencies of materials.

The Density functional theory section of JARVIS (JARVIS-DFT) consists of thousands of VASP based calculations for 3D-bulk, single layer (2D), nanowire (1D) and molecular (0D) systems. Most of the calculations are carried out with optB88vDW functional. JARVIS-DFT includes materials data such as: energetics, diffraction pattern, radial distribution function, band-structure, density of states, carrier effective mass, temperature and carrier concentration dependent thermoelectric properties, elastic constants and gamma-point phonons.

The Machine-learning section of JARVIS (JARVIS-ML) consists of machine learning prediction tools, trained on JARVIS-DFT data. Some of the ML-predictions focus on energetics, heat of formation, GGA/METAGGA bandgaps, bulk and shear modulus.

Tags: automation, classical-interatomic-potential, density-functional-theory, force-field, jarvis, mdcs, mgi, python, restapi
Organization: National Institute of Standards and Technology
Steps to achieve quantitative measurements of microRNA using two-step droplet digital PCR

Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets.  It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods.  However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies.  Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real time PCR (qRT PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods.  False readings are often related to using inadequate enzymes, primers and probes.  Given that two step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT PCR, these barriers are substantial.  Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements.  We have applied two step principles used for miRNA qRT PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits.  We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles.  Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number.  Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments.  Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values.

Tags: biological-measurements, biotechnology, genomics, micrornas, quantitative-analysis, research-and-analysis-methods
Organization: National Institute of Standards and Technology
Supporting Data for Selected Area Electron Beam Induced Deposition of Pt and W for EBSD Backgrounds

These are the unprocessed electron back scatter diffraction patterns (EBSPs) collected from the mesas of electron beam induced deposition (EBID) material, in addition to the Mathematica notebook used to process the images.  Each of the 12 EBID mesa has 10 EBSPs collected at 20 kV and 10 kV, in addition to several longer line scans that step from the silicon substrate onto the EBID mesa.

Tags: background-subtraction, ebid, ebsd, electron-back-scatter-diffraction, electron-beam-induced-deposition, flat-field, pt, w_
Organization: National Institute of Standards and Technology
MCSLinv: An inverse Monte Carlo code  to calculate optical scattering parameters in C++

C++ code for inverse solution of Monte Carlo calculation of optical scattering in single-layer material, i.e., determination of optical scattering parameters from the Angle-Resolved Scattering   Described in RH Streater, A-MR Lieberson, AL Pintar. and ZH Levine, "A parallel version of MCML and an Inverse Monte Carlo Algorithm to Calculate Optical Scattering Parameters," J. Res. NIST, https://doi.org/10.6028/jresnist.122.038.   See also the main article RH Streater, A-MR Lieberson, AL Pintar, CC Cooksey, and P Lemaillet, unpublished.

Tags: mcml-light-scattering-optical-scattering-c-parallel-monte-carlo-inverse-problem
Organization: National Institute of Standards and Technology
MCMLpar:  A parallel version of the MCML code in C++

C++ code for Monte Carlo calculation of optical scattering in multi-layer material.   Described in RH Streater, A-MR Lieberson, AL Pintar. and ZH Levine, "A parallel version of MCML and an Inverse Monte Carlo Algorithm to Calculate Optical Scattering Parameters," J. Res. NIST, https://doi.org/10.6028/jresnist.122.038.   See also the main article RH Streater, A-MR Lieberson, AL Pintar, CC Cooksey, and P Lemaillet, unpublished.

Tags: mcml-light-scattering-optical-scattering-c-parallel-monte-carlo
Organization: National Institute of Standards and Technology
mumpcepy: A Python implementation of the Method of Uncertainty Minimization using Polynomial Chaos Expansions

The Method of Uncertainty Minimization using Polynomial Chaos Expansions (MUM-PCE) was developed as a software tool to constrain physical models against experimental measurements. These models contain parameters that cannot be easily determined from first principles and so must be measured, and some which cannot even be easily measured. In such cases, the models are validated and tuned against a set of global experiments which may depend on the underlying physical parameters in a complex way. The measurement uncertainty will affect the uncertainty in the parameter values.

Tags: experimental-database-experimental-design-optimization-outlier-detection-uncertainty-analysis
Organization: National Institute of Standards and Technology
Thermographic measurements of single and multiple scan tracks on nickel alloy 625 substrates with and without a powder layer in a commercial laser powder bed fusion process (an additive manufacturing technology)

This dataset contains thermographic measurements acquired during single and multiple track scans on bare substrates and on single layers of powder. The substrates and powder are nickel alloy 625 and the experiments are performed inside a commercial laser powder bed fusion machine. There are four experiment cases: 1) a single scan track on a bare substrate, 2) a single scan track on a single hand-spread layer of powder, 3) multiple (39) scan tracks covering an area on a bare substrate, and 4) multiple (39) scan tracks solidifying a single hand-spread layer of powder. Thermographic measurements are performed using a camera system sensitive to wavelengths between 1350 nm and 1600 nm. The camera acquires frames with an integration time of 0.04 ms and a frame rate of 1800 frames per s. The camera signal and radiant temperature values based on a black body calibration are provided. True temperature is not provided because emissivity of the surfaces is unknown. This data was used to measure melt pool length and cooling rate based on radiant temperature as part of the work in: Heigel, J. C. & Lane, B. (2017). "The effect of powder on cooling rate and melt pool length measurements using in situ thermographic techniques." In Proceedings of the 2017 Annual International SFF Symposium (https://www.nist.gov/publications/effect-powder-cooling-rate-and-melt-pool-length-measurements-using-situ-thermographic) 

Tags: additive-manufacturing, cooling-rate, in-625, inconel-625, laser, melt-pool, melt-pool-length, model-validation, nickel-alloy-625, powder-bed-fusion, temperature-measurement, thermography
Organization: National Institute of Standards and Technology
Tables from "Analysis of Pipeline Steel Corrosion Data From NBS (NIST) Studies Conducted Between 1922-1940 and Relevance to Pipeline Management" (NISTIR 7415)

Between 1922 and 1940, the National Bureau of Standards (NBS) conducted a long-term investigation into the corrosion of bare steel and iron, pipes buried underground at 47 sites representing different soil types in the United States. Following the passage of the 2004 Pipeline Safety Improvement Act, the Department of Transportation's Office of Pipeline Safety requested that NIST review and reanalyze the data from the NBS study using modern statistical analysis tools. For this analysis, NIST compiled an updated database from the data in the publications by K. H. Logan (i.e. NBS C450, 1945), M. Romanoff (i.e. NBS C579, 1957), and others, including examination of original logbooks. NIST published a report analyzing this data with modern computer assisted statistical analysis tools (doi.org/10.6028/NIST.IR.7415) and an archival paper summarizing the findings (doi:10.6028/jres.115.026). This data is provided in this format so that others will have the best available data from this research for future analyses.

Tags: corrosion, pipeline, steel, underground
Organization: National Institute of Standards and Technology
Measurement of the Behavior of Steel Beams under Localized Fire Exposure

A total of nine localized fire tests on steel beams were designed and conducted in the National Fire Research Laboratory as part of its commissioning project, including thermal tests (Tests 1 through 5) and four-point bending test at ambient (Test 6) and elevated temperatures (Tests 7 through 9). All the tested specimens were nominally 6.2-m long W16×26 beams made of ASTM A992 steel. Each specimen was supported by one of the two following connections: (i) simple support (Tests 1 through 8), and (ii) double-angles bolted to laterally braced support columns (Test 9). The midspan of each specimen was exposed to an open-flame fire using the 1-m2 natural gas burners. The burner was located 1.1 m below the bottom flange of the beam at midspan. A four-point flexural loading scheme was used to apply concentrated forces at two locations 2.44 m apart around midspan. The data included temperatures, the heat release rates from the burner, and structural measurements including forces, displacements and strains. The Type B standard uncertainties in various measurements were also included. Overall, the test results showed that the heating rate of the specimen was sensitive to the prescribed heat release rate-time relationship. However, the thermal gradient developed in the fire-exposed cross sections of the beam never achieved linearity under the localized fire exposure. Regardless of the connection types and fire conditions (i.e., steady-state or transient-state fire), the beams exhibited a similar behavior and failure mode. When subjected to combined fire and flexural loads, the beam specimens exhibited the lateral-torsional buckling followed by runaway vertical displacements at midspan. Additional details of experimental procedures and uncertainty analysis for this experimental series are provided in the following publications: 1) Zhang, C., Choe, L., Gross, J., Ramesh, S., Bundy, M. (2017). Engineering Approach for Designing a Thermal Test of Real-scale Steel Beam Exposed to Localized Fire. Fire Technology, Vol 53, Issue 4, pp 1535-1554. DOI: 10.1007/s10694-016-0646-7 2) Choe, L., Ramesh, S., Zhang, C., Gross, J. (2016). The Performance of Structural Steel Beams Subjected to a Localized Fire. The 9th International Conference on Structures in Fire (SiF 16), June 8-10, 2016, Princeton, NJ.

Tags: steel-beam-localized-fire-thermal-and-mechanical-behavior-experimental-test
Organization: National Institute of Standards and Technology
Certified values of iodine in CRMs of food matrices in mg/kg units.  The uncertainties are expanded uncertainties at approximately 95% confidence.

A comparison of the expanded uncertainty for certified values of iodine in food matrix CRMs.  The CRMS were found by searching The European Virtual Institute for Speciation Analysis (EVISA) database using the terms "Iodine" and "Certified" in the Material category.  The uncertainties are expanded uncertainties at approximately 95% confidence.

Tags: dietary-supplements, food, food-and-nutrition, nutrition, reference-materials, rm, srm, standard-reference-materials
Organization: National Institute of Standards and Technology
CORR-DATA

Corrosion is defined as the deterioration of a material due to chemical reactions with its environment. Understanding corrosion, and corrosion rates, is necessary to ensure that the design of objects we interact with every day, from the bridges we drive over to the containers used to transport chemicals, from the pipes that carry our water to the utensils we cook with, are safe and perform to specifications.

The Corr-Data dataset was created by the staff of the NACE-NIST Corrosion Data Program. This program was established by a joint agreement between NACE (National Association of Corrosion Engineers) International and NIST (National Institute of Standards and Technology) in Dec. of 1982 and ran until 1997. At its founding, the objective of this program was to provide engineers with software for the then new personal computers that would help them solve corrosion problems. Over the 15 years this program ran, over 20 databases and expert advisory systems for alloys selection were produced and released. While software can go out of date, the data remains relevant. The data describe observations of various samples in potentially corrosive environments under particular conditions (concentrations and temperatures) to see if, how, and at what rate they corrode. The data include over 24,000 records which have been extracted from over 250 different source documents.

The data provided here is from published results, but it should only be considered indicative of how the specified material was observed to perform in the given environment one time. The user needs to keep in mind that corrosion is a highly stochastic process and that behavior can vary greatly with small variations in the environment or material. This data is provided to help users select materials for further evaluation and should not be considered, or construed, as advice on the usability of any material in any environment. Only thoroughly evaluated test results for the whole range of material, loading, and environmental conditions should be used for critical decision making.

Tags: corrosion, nace
Organization: National Institute of Standards and Technology
Effect of Heterogeneity and Shape on Optical Properties of Urban Dust Based on 3-Dimensional Modeling of Individual Particles

This project involves the analysis and modeling of individual urban atmospheric dust particles using scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), focused ion-beam (FIB) tomography, 3-D reconstructions of the particles, and the discrete dipole approximation method for calculating particle optical properties. The particles are heterogeneous in that they have multiple chemical phases. The collected data sets are: 1) element concentrations for selected particles from filter samples using SEM-EDX, 2) element spatial maps of particles using SEM-EDX, 3) secondary electron images from SEM, 4) text files containing information on the locations of chemical phases for each particle based on 3-D reconstructions from FIB tomography, and 5) optical property calculations of particles using the DDA program DDSCAT.

Tags: atmospheric-aerosol, discrete-dipole-approximation, energy-dispersive-x-ray-spectroscopy, fib-sem, fib-tomography, focused-ion-beam-scanning-electron-microscopy, light-scattering, urban-dust
Organization: National Institute of Standards and Technology
Probabilistic distribution of dissolution rate constants for cubic tricalcium aluminate in water

The probabilistic distribution of dissolution rate constants for cubic tricalcium aluminate (C3A) in water was quantified based on in-situ measurements of the changes in the nanoscale surface topography using reflection digital holographic microscopy. Measurements were performed on polished sintered pellets of C3A from two sources. C3A#1 consists of 94.2 % crystalline C3A-c, 2.0 % free CaO, and 3.8 % amorphous content. C3A#2 consists of 84.3 % crystalline C3A-c, 1.0 % free CaO, 4.6 % mayenite, and 10.1 % amorphous content. The data presented in the two text files, labeled C3A#1 and C3A#2, have two columns of values corresponding to the probabilistic distribution (histogram) data; the first column is the frequency and the second column is the rate constant value in units of umol m^-2 s^-1. All uncertainties associated with this dataset are discussed in an accompanying paper.

Tags: dissolution, kinetics, portland-cement, rate-constant, tricalcium-aluminate
Organization: National Institute of Standards and Technology