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252 results for “atomic data”
On Strong Scaling and Open Source Tools for Analyzing Atom Probe Tomography Data
<p>This repository contains supplemental results to the paper "On Strong Scaling and Open Source Tools<br> for Analyzing Atom Probe Tomography Data".</p> <p>Specifically, the input parameter and result files from all synthetic benchmark studies.<br> The results file for all synthetic specimen benchmark studies are available from the<br> authors upon serious request.</p> <p><strong>The repository content is as follows:</strong></p> <p><strong>Real world data:<br> Three triplets of *.tar.gz archive files document the settings and analysis files for the real world case studies</strong><br> 3013902 is the incipient specimen,<br> 2763207 the intermediate specimen, and<br> 3345501 the mature specimen.</p> <p><strong>Scripts.zip</strong><br> Contains all batch scripts we used for performing the analyses as a queue</p> <p><strong>Synthetic data:</strong></p> <p><strong>APTCrystallography.zip</strong><br> Contains all results from the benchmarking of the reimplemented Vicente Araullo-Peters et al. method</p> <p><strong>FullVolumeTessellation.zip</strong><br> Contains all results from the benchmarking of the Voro++ Voronoi volume tessellation method except for the HDF5/XDMF volume tessellation files of the 200 and 2000 million ion datasets</p> <p><strong>TwoPointStatistics.zip</strong><br> Contains all results from benchmarking the computing of 2-point spatial statistics</p> <p><strong>TipSurfaceDescrSpatialStatistics.zip</strong><br> Contains all results from benchmarking the alpha shape computation, descriptive spatial statistics, and clustering analyses</p> <p><strong>PARAPROBE.Results.2Mio.tar.gz<br> PARAPROBE.Results.20Mio.tar.gz</strong><br> <strong>PARAPROBE.Results.200Mio.tar.gz</strong><br> Contains all settings files and some results from benchmarking the hybrid implementation.</p> <p><strong>Unpack the individual repositories using tar through Linux console as follows:</strong><br> tar -xvf <archivename> <br> where <archivename> is a placeholder for the respective tar gz compressed archives within the ZIP file.<br> Alternatively WinRAR can be used on a Windows system.</p> <p><strong>We would kindly like to ask you to use the following repository<br> to access source code of PARAPROBE in the future:</strong></p> <p><strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong><br> <br> <strong>Only above repository will be updated in the future! </strong><br> <strong>Only there new code additions and bugfixes are posted!<br> The examples folder of this repository contains a folder examples/tasks/paper14 which shows how<br> to run a workflow of paraprobe tools from this above repository to run analyses akin as reported in this paper.</strong></p> <p>Recommendations and bug reports to M. Kühbach are appreciated! Happy APT analyzing!</p> <p>------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> <strong>The PARAPROBE source code version we used for analyzing the synthetic and real world APT<br> specimens in the paper used an earlier development version of the PARAPROBE tool, the source code</strong><br> <strong>is here:</strong></p> <p>PARAPROBE_20190117_VersionUsedForPaper.zip</p> <p>https://github.com/mkuehbach/PARAPROBE<br> https://paraprobe.readthedocs.io/en/latest/</p> <p> </p>
Data for "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure"
<p>This upload includes the data presented and analyzed in the article "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure" by Tuomas P. Rossi, Paul Erhart, and Mikael Kuisma.</p> <p>The codes for reproducing the data are provided at <a href="http://doi.org/10.5281/zenodo.3964229">doi:10.5281/zenodo.3964229</a>.</p> <p>See <em>README.md</em> in <em>data.zip</em> for a detailed description.</p>
A phononic crystal coupled to a transmission line via an artificial atom. Experimental data for the article figures
<p>We study a phononic crystal interacting with an articial atom - a superconducting quantum system - in the quantum regime. The phononic crystal is made of a long lattice of narrow metallic stripes on a quatz surface. The articial atom in turn interacts with a transmission line. Therefore, two degrees of freedom of different nature, acoustic and electromagnetic, are coupled with a single quantum object. A scattering spectrum of propagating electromagnetic waves on the articial atom visualizes acoustic modes of the phononic crystal. We simulate the system and found quasinormal modes of our phononic crystal and their properties. The calculations are consistent with the experimentally found modes, which are tted to the dispersion branches of the phononic crystal near the rst Brillouin zone edge. Our geometry allows to realize effects of quantum acoustics on a simple and compact phononic crystal.</p>
Raw Data to "Can Small Polyaromatics Describe Their Larger Counterparts for Local Reactions? A Computational Study on the H-Abstraction Reaction by an H-Atom from Polyaromatics"
<p>This data includes the Turbomole input files (without molecular orbitals) and output files (under <strong> DFT_and_CC_*tar</strong>) as well as the output of the xTB calculations (under <strong>xtb*tar</strong>) for different reactive sites of the polyaromatics (PAHs) studied in the related publication, for the reaction:<br> C<sub>X</sub>H<sub>Y</sub> + H -> C<sub>X</sub>H<sub>Y-1</sub> + H<sub>2</sub><br> <br> <strong>File structure:</strong></p> <ul> <li>The xtb*tar contains the xTB (xTB version 6.3.1) optimized structures for the parameterizations <strong>GFN0</strong>, <strong>GFN1</strong> and <strong>GFN2</strong>. The parameter set is indicated by the folder name "<strong>BACK_XTB_NATIVE_GFN0</strong>", "<strong>BACK_XTB_NATIVE_GFN1</strong>" and "<strong>BACK_XTB_NATIVE_GFN2</strong>"<br> </li> <li>The DFT calculations are carried out at the <strong>TPSSh-D3/TZVP </strong>level and they are directly under the subdirectories of dft*tar folders (C*H*) and are used to calculate the data under <strong>Figure 3</strong> and <strong>4</strong> of the related publication, as well as to calculate partition functions which are listed under <strong>freeh.out</strong>,<strong> </strong>the output of the freeh program of Turbomole.<br> </li> <li>The coupled cluster calculations are always located under the subdirectories of the DFT calculations.<br> </li> <li>The subdirectories <strong>PNO-CC.tz</strong> are <strong>PNO-CCSD/cc-pVTZ</strong> calculations and the output files are named as 'pnoccsd.out.tpno.7' or 'pnoccsd.out.tpno.8', where 7 and 8 stands for the PNO selection thresholds of 10<sup>-7 </sup>and 10<sup>-8</sup>, which are used to produce the data under <strong>Table 11</strong> of the related publication.<br> </li> <li>The subdirectories <strong>CC.atz.f12</strong>, <strong>CC.dz</strong>, and <strong>CC.tz</strong> under<strong> </strong>C6H6* and C10H8* correspond to <strong>R(O)HF-CCSD(F12*)(T)/aug-cc-pVTZ</strong>, <strong>R(O)HF-CCSD(T)/cc-pvDZ </strong>and <strong>R(O)HF-CCSD(T)/cc-pvTZ </strong>calculations respectively, which is used for the calculation of the data under <strong>Table</strong> <strong>10</strong> of the related publication.<br> </li> <li>The subdirectories <strong>UHF-CC.atz.f12</strong> under C6H6-* and C10H8-* include <strong>UHF-CCSD(F12*)(T)/aug-cc-pVTZ </strong>calculations for the transition states and the products. The subdirectories <strong>CC.atz.f12 </strong>under C6H6 and C10H8 include <strong>RHF-CCSD(F12*)(T)/aug-cc-pVTZ</strong> calculations for the reactants benzene and naphthalene.<strong> </strong>These are used to calculate the data under <strong>Table 9</strong> in the related publication<br> </li> <li>The subdirectories <strong>rij.grid_m3.scfconv_7</strong> under C14H10* includes the DFT calculations with m3 integration grid and RI-J approximation. Under these, the subfolders <strong>(UHF-)PNO-CC.atz.f12</strong> include the <strong>PNO-(UHF-)CCSD(F12*)(T)/aug-cc-pVTZ</strong> calculations which are used to produce the data under <strong>Table 9</strong> in the related publication.<br> </li> <li>The subdirectories <strong>(UHF-)PNO-CC.atz.f12</strong> under C6H6* and C10H8* include<strong> PNO-(UHF-)CCSD(F12*)(T)/aug-cc-pVTZ</strong> calculations which are used for<strong> PNO threshold selection</strong> for the UHF-CCSD(F12*)(T) calculations (<strong>Table S2 </strong>of the Supporting Information of the related publication).</li> </ul>
AFM data of ice clusters on Cu(111) and Au(111) in paper "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Frequency shift CO-tip atomic force microscopy data of small ice clusters on Cu(111) and Au(111) surfaces as they appear in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains each experiment as a Numpy .npz file. Each file contains the measurement data as a 3D array in the key 'data' and the physical extent of the scan region in the x and y directions in Ånströms in the keys 'lengthX' and 'lengthY'.</p>
Data for "Atomic physics on a 50 nm scale: Realization of a bilayer system of dipolar atoms"
<p>One can find:</p> <p>(1) The tabular data for every plot in the main article and the supplementary material of "Atomic physics on a 50 nm scale: Realization of a bilayer system of dipolar atoms" (arXiv:2302.07209).</p> <p>(2) The Mathematica and Jupyter notebook files for generating theoretical curves and for analyzing experimental data.</p>
Data for the paper "Microcanonical and canonical fluctuations in atomic Bose-Einstein condensates – Fock state sampling approach"
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Research data for "Understanding Defects in Amorphous Silicon with Million-Atom Simulations and Machine Learning"
<p>This dataset contains structural data and ML local energies for the publication "Understanding Defects in Amorphous Silicon with Million-Atom Simulations and Machine Learning". Details of the contents can be found in README.txt. Code to analyse structures and reproduce figures from the publication are available at https://github.com/MorrowChem/understanding_defects</p>
Atomic data for SIKE
<div> <p>This is a repository of atomic data (levels, transitions, cross-sections, etc) for use with the atomic kinetic solver SIKE (https://github.com/plasdom/SIKE). This is used for calculating equilibrium atomic state distributions in magnetic fusion plasmas with impurities. </p> <p>It has been assembled with inputs from:<br>- FAC (Gu, M. Canadian Journal of Physics (2004))<br>- FLYCHK (Chung, H. et al. High Energy Density Physics (2005))</p> <p> </p> <p>See the following preprint for further details: https://arxiv.org/abs/2410.00651</p> </div>
Computational Data: Accurately computed dimerization trends of ALD precursors and their impact on surface reactivity in area-selective atomic layer deposition
<p><span>The Lewis acidic nature of aluminum atoms in common precursors for the atomic layer deposition (ALD) of Al<sub>2</sub>O<sub>3</sub> can lead to dimerization. This study investigates whether these compounds predominantly exist as monomers or dimers under ALD conditions. Understanding dimerization is crucial for discussing precursor reactivities and other properties, especially in the context of area-selective ALD (AS-ALD). We employed a theoretical approach, incorporating conformer search, density functional theory, and coupled cluster calculations, to determine the dissociated dimer fraction for a range of precursors under typical ALD pressures and temperatures. The precursors studied include aluminum alkyls, chlorinated aluminum alkyls, dimethylaluminumisopropoxide (DMAI), and trisdimethylamidoaluminum (TDMAA). Our findings indicate that aluminum alkyls are completely dissociated over the whole parameter range, while DMAI and TDMAA form stable dimers. Chlorinated precursors were found to exist in both monomeric and dimeric forms depending on temperature and pressure.</span></p>
Data and code for "Hydrogen-driven Surface Segregation in Pd-alloys from Atomic Scale Simulations"
<p>This record contains data and scripts pertaining to the publication "Hydrogen-driven Surface Segregation in Pd-alloys from Atomic Scale Simulations".</p>
Raw data repository for the article: "Spatially resolved fluorescence of caesium lead halide perovskite supercrystals reveals quasi-atomic behavior of nanocrystals"
<p>Raw data depository for the article in Nature Communications journal: <a href="https://doi.org/10.1038/s41467-022-28486-3">DOI: 10.1038/s41467-022-28486-3</a>. Details and the file description are given in the file "Lapkin_Dataset_Info.pdf"</p>
Source data and codes for the paper "Inviting atomic mechanics to macro-continua: A study on monocrystalline Si using a spatial multilevel coarsening model"
<p>Source data and codes for the paper "Inviting atomic mechanics to macro-continua: A study on monocrystalline Si using a spatial multilevel coarsening model"</p> <p>This file includes </p> <p>- Source data for Figs 1-5 and Supplementary Materials</p> <p>- LAMMPS codes and raw log files used to produce the results of this study</p> <p> </p>
Data for 'Experimental Determination of a Single Atom Ground State Orbital through Hyperfine Anisotropy'
<p>This folder contains the raw data and scripts used for the paper <em>'Experimental Determination of a Single Atom Ground State Orbital through Hyperfine Anisotropy'</em>.</p>
Simulation Input Data for "Atomic Origins of Biomass Recalcitrance in Organic Solvents"
<p>This is the reduced data behind an upcoming manuscript investigating lignocellulosic interactions in plant secondary wall, when exposed to different organic solvent pretreatment. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:</p> <pre><code class="language-bash">tar -zcvf lignincelluloseindustrialsolvent.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*log" --exclude="*[0-9].out" --exclude="*npz" --exclude="*pkl" --exclude="*npy" --exclude="*png" --exclude="*bmim*" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*txt" --exclude="*state_prev.cpt" --exclude="*ppm" --exclude="Simulations" FaceDifferences</code></pre> <p>Within the FaceDifferences directory, there are 2 primary subdirectories:</p> <ul> <li><strong>Build </strong>contains the scripts and files to build the individual lignin cellulose in organic solvent molecular systems.</li> <li><strong>NewSolventSimulations</strong> contains the all-atom MD simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>)</li> </ul>
Data from: Atomic-vapor magnetometer in a laser-written micro-channel
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Data for droplet frequencies in atomizing pulsed jet
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Scripts and data from the study 'Characterisation of magnetic atomic and molecular beamlines for the extraction of empirical scattering-matrices' (PCCP manuscript number CP-ART-04-2024-001785)
<p>This repository contains the data used for the article "Characterisation of magnetic atomic and molecular beamlines for the extraction of empirical scattering-matrices" and includes the code for generating the figures in the publication.</p>
Indistinguishable photons from an artificial atom in silicon photonics [Data]
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IR data of the compounds published in "Replacement of Molybdenum by Tungsten in a Biomimetic Complex Leads to an Increase in Oxygen Atom Transfer Catalytic Activity"
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.