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Trinamic TMCL IOC is a Python package designed for controlling stepper motors connected to a Trinamic board using the TMCL language (all boards supported by PyTrinamic should now work, has been tested on the TMCM 6110 and the TMCM 6214). Since it is implementing the TMCL protocol, it should be easy to adapt to other Trinamic motor controller boards. This package assumes the motor controller is connected over a machine network via a network-to-serial converter, but the underlying PyTrinamic package allows for other connections too.
This allows the control of attached motors via the EPICS Channel-Access virtual communications bus. If EPICS is not desired, plain Pythonic control via motion_control should also be possible. An example for this will be provided in the example.ipynb Jupyter notebook.
This package leverages Caproto for EPICS IOCs and a modified PyTrinamic library for the motor board control, and interfaces between the two via an internal set of dataclasses. Configuration for the motors and boards are loaded from YAML files (see tests/testdata/example_config.yaml).
The modifications to PyTrinamic involved extending their library with a socket interface. This was a minor modification that should eventually find its way into the official package (a pull request has been submitted).
This is a set of use examples for the HDF5Translator framework. This framework lets you translate measurement files into a different (e.g. NeXus-compatible) structure, with some optional checks and conversions on the way. For an in-depth look at what it does, there is a blog post here.
The use examples provided herein are each accompanied by the measurement data necessary to test and replicate the conversion. The README.md files in each example show the steps necessary to do the conversion for each.
We encourage those who have used or adapted one or more of these exampes to create their own conversion, to get in touch with us so we may add your example to the set.
Jobflow is a free, open-source library for writing and executing workflows. Complex workflows can be defined using simple python functions and executed locally or on arbitrary computing resources using the FireWorks workflow manager.
Some features that distinguish jobflow are dynamic workflows, easy compositing and connecting of workflows, and the ability to store workflow outputs across multiple databases.
This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (https://doi.org/10.1039/D2CP05053F).
Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included.
TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry which is further described in https://doi.org/10.26272/opus4-55751.
This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission.
Simulates X-ray and Neutron scattering patterns from arbitrary shapes defined by STL files.
Features:
- Uses multithreading to compute a number of independent solutions, then uses the variance of the results to estimate an uncertainty on the output.
- Can be launched from the command line using an excel sheet to define settings, or from a jupyter notebook.
- Outputs scattering patterns in absolute units if the contrast is set.
- A Gaussian size distribution is available, where the relative scaling of objects for each repetion can be varied. Recommended to be used with limited width (max. 10%) to avoid artefacts.
- Writes results with settings to an archival HDF5 file.
Application examples:
This software has been used in several studies to date. For example, it has been used here to simulate a model scattering pattern for a cuboid shape, which was then fed forward into the McSAS3 analysis program for analyzing scattering patterns of polydisperse cuboids. A second use is here, where it was used for the modeling of flattened helices. In this paper, scattering pattern features could be matched with particular morphological changes in the structure. Lastly, this paper has an example where it was used to validate the analytical analysis model, and explore the realistic limits of application of the analytical model.
2PP-TestArtifact
(2023)
This repository contains a test artifact (TA), also called test structure, designed for two-photon polymerization (also known as Direct Laser Writing (DLW) or Two/Multi-photon lithography (2PA/MPA)). Test artifacts can be used to compare structures, to check options used by the slicer, check the state of the 2PP machine itself or to get a construction guidelines for a certain combination of power, velocity and settings.
The associated paper can be found here: https://dx.doi.org/10.1088/1361-6501/acc47a
General ideas behind the test artifact:
1. optimized for 2PP-DLW
2. should be fast and easy to analyse with optical microscopy or 3. scanning electron microscopy without tilt.
3. short time to fabricate
4. include a reasonable amount of different features
5. bulk and small structures on the substrate
This dataset is a complete set of raw, processed and analyzed data, associated with the manuscript mentioned in the title.
All associated metadata and processing history has been added. Particle size distribution analyses using McSAS are included as well.
The samples consisted of a 4.2 mass% dispersion of yttria-stabilized zirconia nanoparticles in a cross-linked matrix. The measurements show a good dispersion with minimal agglomeration. The wide-angle region shows diffraction information consistent with zirconia.
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”.
McSAS3
(2023)
McSAS3 is a refactored version of the original McSAS (see DOI 10.1107/S1600576715007347). This software fits scattering patterns to obtain size distributions without assumptions on the size distribution form. The refactored version has some neat features:
- Multiprocessing is included, spread out over as many cores as number of repetitions!
- Full state of the optimization is stored in an organized HDF5 state file.
- Histogramming is separate from optimization and a result can be re-histogrammed as many times as desired.
- SasModels allow a wide range of models to be used
- If SasModels does not work (e.g. because of gcc compiler issues on Windows or Mac), an internal sphere model is supplied
- Simulated data of the scattering of a special shape can also be used as a McSAS fitting model. Your models are infinite!
- 2D fitting also works.
These are four datasets that were made available to the participants of the Small-angle Scattering data analysis round robin. The intent was to find out how comparable results from different researchers are, who analyse exactly the same processed, corrected dataset.
In this repository, there are:
1) a PDF document with more details for the study,
2) the datasets for people to try and fit
3) an Excel spreadsheet to document the results.
Datasets 1 and 2 were modified from: Deumer, Jerome, & Gollwitzer, Christian. (2022). npSize_SAXS_data_PTB (Version 5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5886834
Datasets 3 and 4 were collected in-house on the MOUSE instrument.
SASfit 0.94.12
(2023)
Small-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields.
The datasets from (Hard Energy) X-ray photoelectron spectroscopy, X-ray diffraction and Scanning Electron Microsopy are related to the publication
G. Chemello, X. Knigge, D. Ciornii, B.P. Reed, A.J. Pollard, C.A. Clifford, T. Howe, N. Vyas, V.-D. Hodoroaba, J. Radnik
"Influence of the morphology on the functionalization of graphene nanoplatelets analyzed by comparative photoelectron spectroscopy with soft and hard X-rays"
Advanced Materials Interfaces (2023), DOI: 10.1002/admi.202300116.
Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. This open-source software package powers the Materials Project.
In this particular contribution, the handling of obital-resolved "ICOHPLIST.lobster" files from Lobster was implemented in the software package (github handle: @JaGeo).
This database consists of bonding data computed using Lobster for 1520 solid-state compounds consisting of insulators and semiconductors. It consists of two kinds of json files. Smaller lightweight JSONS consists of summarized bonding information for each of the compounds. The files are named as per ID numbers in the materials project database.
Here we provide also the larger computational data json files for 700 compounds. This files consists of all important LOBSTER computation output files data stored as dictionary.
This database consists of bonding data computed using Lobster for 1520 solid-state compounds consisting of insulators and semiconductors. The files are named as per ID numbers in the materials project database.
Here we provide the larger computational data JSON files for the rest of the 820 compounds. This file consists of all important LOBSTER computation output files data stored as a dictionary.
## Summary:
This notebook and associated datasets (including VASP details) accompany a manuscript available on the ArXiv (https://doi.org/10.48550/arXiv.2303.13435) and hopefully soon in a journal as short communication as well. Most of the details needed to understand this notebook are explained in that paper with the same title as above. For convenience, the abstract is repeated here:
## Paper abstract:
We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is presented coupled to the scattering intensity, may offer a novel pathway for determining the degree of crystallinity.
The ``Ultima Ratio'' strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from $Q<0.01$\,$\mathrm{nm}^{-1}$ up to $Q\approx150$\,$\mathrm{nm}^{-1}$, with a resolution of 0.16\,\AA. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to $8000^3$ voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-$Q$ behaviour.
The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder.
While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts.
Electric Safety Interlock
(2023)
This interlock is designed to prevent electrical shock from high voltage (>60V) equipment.
While the general safety interlock can be generically applied, this particular example employs an external vacuum-activated switch. It is for safeguarding human operations inside a vacuum sample chamber while the chamber doors are open. The circuit is closed (output is active) when a sufficient level of vacuum is reached, i.e. when all accessible openings are necessarily closed.
The initial application is to interrupt power to a 220V, 250W heating cartridge (itself mounted inside a small sample holder with potentially exposed contacts) when the sample chamber is open.
The external circuit can be modified to use different interlock mechanisms as needed. Note that the external interlock circuit is only a single circuit (with two signal lines) and thus is not protected against external shorts.
To accomodate a range of safety interlocks, the 4-pin M12 connector is wired as follows: Pin 1 (Brown): +24V for power supply, max current 0.6A Pin 2 (White): Safety interlock system signal 1 (0 or 24V) Pin 3 (Blue) : Safety interlock system signal 2 (0 or 24V) Pin 4 (Black): 0V for power supply
The safety is interlocked (output active) when both signal pins are set high (24V), with sufficient current to activate the two relays. Pin 1 and 4 can be used to power safety hardware (such as light curtains or proximity detectors) with 24VDC up to a current of 0.6A. A larger power supply can be installed when higher currents are needed, while staying within the current limits imposed by the wiring cross-section.
Test artifact for fs-LDW
(2023)
Wide-range X-ray scattering datasets and analyses for all samples described in the 2020 publication "Gold and silver dichroic nanocomposite in the quest for 3D printing the Lycurgus cup". These datasets are composed by combining multiple small-angle x-ray scattering and wide-angle x-ray scattering curves into a single dataset. They have been analyzed using McSAS to extract polydispersities and volume fractions. They have been collected using the MOUSE project (instrument and methodology).
SI Files for "Towards automation of the polyol process for the synthesis of silver nanoparticles"
(2022)
The graphml file: reaction_graph_AgNP.graphml is included. It contains topological information (Fig. 1 in the main text) about the reaction setup and metadata with reaction condtions. It used by the Python API used to control the Chemputer.
SAXS reports. The complete report sheets generated by McSAS are included. They contain extended information characterising the size distributions and the fitting parameters.
NP3_I: saxs_report_NP3_I.pdf
NP3_II: saxs_report_NP3_II.pdf
NP3_III: saxs_report_NP3_III.pdf
NP3_IV: saxs_report_NP3_IV.pdf
NP5_I: saxs_report_NP5_I.pdf
NP5_II: saxs_report_NP5_II.pdf
NP5_III: saxs_report_NP5_III.pdf
In recent years, we have come to appreciate the astounding intricacy of the formation process of minerals from ions in aqueous solutions. In this context, a number of studies have revealed that nucleation in the calcium sulfate system is non-classical, involving the aggregation and reorganization of nanosized prenucleation particles. In a recent work we have shown that this particle-mediated nucleation pathway is actually imprinted in the resultant single micron-sized CaSO4 crystals. This property of CaSO4 minerals provides us with an unique opportunity to search for evidence of non-classical nucleation pathways in geological environments. In particular, we focused on the quintessential single crystals of anhydrite extracted from the Naica mine in Mexico. We elucidated the growth history from this mineral sample by mapping growth defects at different length scales. Based on these data we argue that the nano-scale misalignment of the structural sub-units observed in the initial calcium sulfate crystal seed propagate through different length-scales both in morphological, as well as strictly crystallographic aspects, eventually causing the formation of large mesostructured single crystals of anhydrite. Hence, the nanoparticle mediated nucleation mechanism introduces a 'seed of imperfection', which leads to a macroscopic single crystal, in which its fragments do not fit together at different length-scales in a self-similar manner. Consequently, anisotropic voids of various sizes are formed with very well-defined walls/edges. But, at the same time the material retains its essential single crystal nature. These findings shed new light on the longstanding concept of crystal structure.
This dataset accompanies the following publication, first published in Scientific Reports (www.nature.com/articles/s41598-021-84287-6):
B. Ruehle, J. Krumrey, V.-D. Hodoroaba, Scientific Reports, Workflow towards Automated Segmentation of Agglomerated, Non-Spherical Particles from Electron Microscopy Images using Artificial Neural Networks, DOI: 10.1038/s41598-021-84287-6
It contains electron microscopy micrographs of TiO2 particles, the corresponding segmentation masks, and their classifications into different categories depending on their visibility/occlusion. Please refer to the publication and its supporting information for more details on the acquisition and contents of the dataset, as well as the GitHub repository at https://github.com/BAMresearch/automatic-sem-image-segmentation
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 is a complete set of raw, processed and analyzed data, complete with Jupiter notebooks, associated with the manuscript mentioned in the title.
In the manuscript, we provide a "systems architecture"-like overview and detailed discussions of the methodological and instrumental components that, together, comprise the "MOUSE" project (Methodology Optimization for Ultrafine Structure Exploration). Through this project, we aim to provide a comprehensive methodology for obtaining the highest quality X-ray scattering information (at small and wide angles) from measurements on materials science samples.
Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite", by Paulina Szymoniak, Brian R. Pauw, Xintong Qu, and Andreas Schönhals.
Datasets are in three-column ascii (processed and azimuthally averaged data) from a Xenocs NanoInXider SW instrument. Monte-Carlo analyses were performed using McSAS 1.3.1, other analyses are in the Python 3.7 worksheet. Graphics and result tables are output by the worksheet.
This is the repository of all experimental raw data used in the Scientific Reports publication "Specific adsorption sites and conditions derived by thermal decomposition of activated carbons and adsorbed carbamazepine" by Daniel Dittmann, Paul Eisentraut, Caroline Goedecke, Yosri Wiesner, Martin Jekel, Aki Sebastian Ruhl, and Ulrike Braun.
It includes
- overview_measurements.xlsx and overview_measurements.ods containing a list of all TGA experiments (TGA, TGA-FTIR, TED-GC-MS, and ramp-kinetics)
- TED-GC-MS.zip containing gas chromatography-mass spectrometry experimtent files for the Chemstation and OpenChrom
- TGA.zip containing thermogravimetric analyses raw data on evolved gas analyses experiments (TGA-FTIR and TED-GC-MS)
- TGA_kinetics.zip containing thermogravimetric analyses raw data on decomposition kinetic experiments (ramp-kinetics)
- TGA-FTIR.zip containing Fourier-transform infrared spectroscopy series files for OMNIC
- XRF.zip containing x-ray flourescence data on elemental composition