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This tutorial is aimed at developers who would like to develop workflows with Jobflow. This could include contributions to atomate2 and quacc. Jobflow workflows can also be executed with Fireworks on Supercomputers.
This tutorial includes information on how to write a job for jobflows, how to connect jobs to a workflow including dynamic features and how to store job results in databases. The structure of the workflow is inspired by workflows that have been developed for atomate2 and quacc.
This tutorial is also connected to google collab so that you can execute the code via their services.
Please access the tutorial here: https://jageo.github.io/Advanced_Jobflow_Tutorial/intro.html
This file contains all the data used for the figures shown in the Dissertation of Ruben Gerrits with the title "An experimental study of fungal olivine weathering".
In this study, the weathering-affecting, rock-inhabiting fungus, Knufia petricola A95 and the Fe-bearing olivine (Fe0.2Mg1.8SiO4) were selected to investigate fungi-induced effects on mineral dissolution. The availability of a melanin-deficient mutant (ΔKppks) of K. petricola A95, that produced more extracellular polymeric substances (EPS) than the wild type (WT), enabled comparative studies of the role of melanin and EPS in weathering processes.
This dataset contains raw data resulting from Impact-Echo measurements at the reference concrete block "IE Platte", located at BAM (German Federal Institute for Materials Research and Testing).
The specimen contains three polystyrene slabs and one polyethylene foil to act as reflectors. The specimen was produced in a three-step process. First, the base plate was cast. Second, the reflectors were taped to the base plate. Finally, the upper layer was cast on top of base plate and reflectors. A drawing is contained in the dataset.
The Impact-Echo method is based on the excitation of the zero-group-velocity frequency of the first symmetric Lamb mode of a plate-like structure, in order to assess its thickness. Numerous publications elaborate on Impact-Echo theory, examples are (Gibson and Popovics 2005, Schubert and Köhler 2008 , Abraham and Popovics 2010).
The measurements have been conducted using a setup that contains only commercially available components. The setup consists of an Olson CTG-2 concrete thickness gauge (Olsen Instruments, USA) for actuation and sensing and an 8-bit NI USB-5132 digital storage oscilloscope (National Instruments, USA) combined with the Echolyst software (Schweizerischer Verein für technische Inspektionen (SVTI), Switzerland) for data acquisition.
Measurements were conducted using a grid of 29x29 points with a spacing of 50 mm. At each point 8192 samples were recorded at a sampling rate of 1 MS/s.
The dataset contains the (X,Y) location in mm of the individual measurement points as well as the raw measurement data at those points.
The data is provided in the formats *.mir/*.mhdr (Echolyst), *.npy (Python) and *.mat (Matlab) and *.csv to ease the import in various post-processing tools.
Models for TOPAS/Geant4 to estimate the microscopic dose received by biomolecules during bioSAXS experiments.
The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) Monte-Carlo program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org).
These files contain cell models for TOPAS/Geant4 and the inclusion of nano particles in particle scattering simulations. A simple spherical cell with nanoparticles can be generated in a fast manner. The user has the option to include the following organelles: nucleus, mitochondria, cell membrane. Additionally nanoparticles can be included in the cytosol and at the surface of the nucleus and/or the mitochondria.
The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) Monte-Carlo program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org). The sourcecode together with examples and scorers are provided.
"If you use this extension please cite the following literature:
Hahn, M.B., Zutta Villate, J.M. "Combined cell and nanoparticle models for TOPAS to study radiation dose enhancement in cell organelles." Sci Rep 11, 6721 (2021).
https://doi.org/10.1038/s41598-021-85964-2 "
To simulate the movement of the macroscopic magnetic moment in ferromagnetic systems under the influence of elevated temperatures, the stochastic version of the Landau-Lifshitz (LL) or the Landau-Lifshitz-Gilbert equation with a spin density of one per unit cell has to be used.
To apply the stochastic LL to micromagnetic simulations, where the spin density per unit cell is generally higher, a conversion has to be performed. OOMMF sample files MIF) are provided which can be used to determine the Curie temperature for the classical bulk magnets, iron, nickel and cobalt.
This dataset represents the electronic supplementary material (ESM) of the publication entitled "Characterisation of conventional 87Sr/86Sr isotope ratios in cement, limestone and slate reference materials based on an interlaboratory comparison study", which is published in Geostandards and Geoanalytical Research under the DOI: 10.1111/GGR.12517. It consists of four files. 'ESM_Data.xlsx' contains all reported data of the participants, a description of the applied analytical procedures, basic calculations, the consensus values, and part of the uncertainty assessment. 'ESM_Figure-S1' displays a schematic on how measurements, sequences and replicates are treated for the uncertainty calculation carried out by PTB. 'ESM_Technical-protocol.pdf' is the technical protocol of the interlaboratory comparison, which has been provided to all participants together with the samples and which contains bedside others the definition of the measurand and guidelines for data assessment and calculations. 'ESM_Reporting-template.xlsx' is the Excel template which has been submitted to all participants for reporting their results within the interlaboratory comparison. Excel files with names of the the structure 'GeoReM_Material_Sr8786_Date.xlsx' represent the Rcon(87Sr/86Sr) data for a specific reference material downloaded from GeoReM at the specified date, e.g. 'GeoReM_IAPSO_Sr8786_20221115.xlsx' contains all Rcon(87Sr/86Sr) data for the IAPSO seawater standard listed in GeoReM until 15 November 2022.
Data set of low-field NMR spectra of continuous synthesis of nitro-4’-methyldiphenylamine (MNDPA). 1H spectra (43 MHz) were recorded as single scans.
Two different approaches for the generation of artificial neural networks training data for the prediction of reactant concentrations were used: (i) Training data based on combinations of measured pure component spectra and (ii) Training data based on a spectral model.
Synthetic low-field NMR spectra
First 4 columns in MAT-files represent component areas of each reactant within the synthetic mixture spectrum.
Xi (“pure component spectra dataset”)
Xii (“spectral model dataset”)
Experimental low-field NMR spectra from MNDPA-Synthesis
This data set represents low-field NMR-spectra recorded during continuous synthesis of nitro-4’-methyldiphenylamine (MNDPA). Reference values from high-field NMR results are included.
In case study one of the CONSENS project, two aromatic substances were coupled by a lithiation reaction, which is a prominent example in pharmaceutical industry. The two aromatic reactants (Aniline and o-FNB) were mixed with Lithium-base (LiHMDS) in a continuous modular plant to produce the desired product (Li-NDPA) and a salt (LiF). The salt precipitates which leads to the formation of particles. The feed streams were subject to variation to drive the plant to its optimum.
The uploaded data comprises the results from four days during continuous plant operation time. Each day is denoted from day 1-4 and represents the dates 2017-09-26, 2017-09-28, 2017-10-10, 2017-10-17.
In the following the contents of the files are explained.
Related work
Laboratory Study:
Combining Signal Features of Ground-Penetrating Radar to Classify Moisture Damage in Layered Building Floors
https://doi.org/10.3390/app11198820
On-Site Study:
TBA
Doctoral Thesis:
Non-destructive classification of moisture deterioration in layered building floors using ground penetrating radar
https://doi.org/10.14279/depositonce-19306
Measurement Parameters
The GPR measurements were carried out with the SIR 20 from GSSI and a 2 GHz antenna pair (bandwidth 1 GHz to 3 GHz) in common-offset configuration. Each B-Scan consists of N A-Scans, each including 512 samples of a 11 ns time window. Survey lines were recorded with 250 A-Scans/ meter, which equals a 4 mm spacing between each A-Scan No Gains were applied.
Folder Description:
Lab_dry, Lab_insulDamage, Lab_screedDamage
- each contain 168 Measurements (B-Scans) in .csv on 84 dry floors, floors with insulation damage and screed damage.
- each floor setup was measured twice on two orthogonal survey lines, indicated by _Line1_ and _Line2_ in the file name.
- the file names encode the building floor setup e.g. CT50XP100 describes a 50 mm cement screed with 100 mm extruded polystyrene below
- the material codes are
CT: cement screed, CA: anhydrite screed, EP: expanded polystyrene, XP: extruded polystyrene, GW: glass wool, PS: perlites
further information can be found in the publication https://doi.org/10.3390/app11198820
OnSite_
- 5 folders containing B-Scans on 5 different practical moisture damages
- the building floor setup is encoded according to the lab with an additional measurement point numbering at the start and a damage case annotation at the end of the file name with _dry, _insulationDamage and_screedDamage
File Description:
B-Scans, Measurement files - no header
- dimension: 512 x N data point with N beeing the number of A-Scans including 512 samples of a 11 ns time window.
- survey lines were recorded with 250 A-Scans/ meter, which equals a 4 mm spacing between each A-Scan
Moisture References
- Moist_Reference of On-Site Locations include the columns MeasPoint: Measurement point, wt%Screed: moisture content of screed layer in mass percent; wt%Insul: moisture content of insulation layer in mass percent. References were obtained by drilling cores with 68 mm diameter in the center of each survey line.
- Moist_Reference_Screed of Lab data include the columns Screed: Screed material and thickness in mm, wt%Screed moisture content of screed layer in mass percent
- Moist Reference_Insul of Lab data include the columns Insulation: Insulation material and thickness in mm, water addition in l: water added to the insulation layer in liters, V%Insulation: water added to the insulation layer in volume percent, RH%: resulting relative humidy in the insulation layer during measurement. These References are only avaible for Lab measurements on insulation damages.
Here a dataset of XPS, HAXPES and SEM measurements for the physico-chemical characterization of Au nanoparticles is presented. The measurements are part of the H2020 project “NanoSolveIT”.
Here a dataset of XPS, HAXPES and SEM measurements for the physico-chemical characterization of Fe3O4 nanoparticles is presented. The measurements are part of the H2020 project “NanoSolveIT”.