Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
125
datasets available to search
ShareScore release 0.9.0
Dataset results
125 results for “model transfer”
Model output used in the manuscript "Seasonality in carbon flux attenuation explains spatial variability in transfer efficiency"
<p>This *.zip file contains the model output from seasonal variability experiments using the NPZD-DOP GEOMAR biogeochemical model (<a href="https://doi.org/10.1016/j.pocean.2010.05.002" target="_blank" rel="noopener">Kriest et al., 2010</a>) coupled with the MITgcm 2.8deg ocean circulation via the transport matrix method (<a href="https://doi.org/10.1016/j.ocemod.2004.04.002" target="_blank" rel="noopener">Khatiwala et al., 2005</a>; <a href="https://doi.org/10.1029/2007GB002923" target="_blank" rel="noopener">Khatiwala, 2007</a>; <a href="https://doi.org/10.5281/zenodo.1246300" target="_blank" rel="noopener">Khatiwala, 2018</a>).</p> <p>These model outputs are presented and discussed in the Preprint "<em>Seasonality in carbon flux attenuation explains spatial variability in transfer efficiency</em>", published by Geophysical Research Letters (<a href="https://doi.org/10.1029/2023GL107050" target="_blank" rel="noopener">de Melo Viríssimo et al., 2024</a>). The manuscript describes the experiments performed, the parameter values used and the modifications done to the original model. For this matter, we also refer you to <a href="https://doi.org/10.1029/2021GB007101" target="_blank" rel="noopener">de Melo Viríssimo et al. (2022)</a>.</p> <p>All files uploaded were generated from simulations run by the authors, except: the grid file, the salinity field, and the temperature field, which came with the model; and the density fields, who were computed from the MITgcm 2.8deg transport matrix by Dr Rafaelle Bernadello, using a TEOS-10 Matlab routine (<a href="http://www.teos-10.org/">http://www.teos-10.org/</a>).</p> <p>For specific information about each file uploaded, please refer to the README file. If you have any questions, please feel free to contact me.</p>
Radiance data for "Systematic Comparison of Vectorial Spherical Radiative Transfer Models in Limb Scattering Geometry" by Zawada et al.
<p>Radiance data for "Systematic Comparison of Vectorial Spherical Radiative Transfer Models in Limb Scattering Geometry" by Zawada et al. which is to be submitted to Atmospheric Measurement Techniques. </p> <p>A comprehensive inter-comparison of seven radiative transfer models in the limb scattering geometry has been<br> performed. Every model is capable of accounting for polarisation within a fully spherical atmosphere. Three models (GSLS, SASKTRAN-HR, and SCIATRAN) are deterministic, and four models (MYSTIC, SASKTRAN-MC, Siro, and SMART-G)<br> are statistical using the Monte Carlo technique. This dataset consists of the raw radiance data used to perform the intercomparisons, atmospheric input data for the optical properties of the atmosphere, and data specifying the geometry of the test cases.</p> <p>Data is provided in NetCDF4 format with documentation present inside the variable attributes.</p> <p>More detail on the comparison scenarios can be found within the published article. (Link to be added when available).</p>
Radiative transfer modeling in structurally-complex stands: what aspects matter most?: Dataset
<p>This repository is linked to the paper "Radiative transfer modeling in structurally-complex stands: what aspects matter most?" submitted to Annals of Forest Science and written by Frédéric ANDRÉ (corresponding author), Louis DE WERGIFOSSE, François DE COLIGNY, Nicolas BEUDEZ, Gauthier LIGOT, Vincent GAUTHRAY-GUYÉNET, Benoit COURBAUD and Mathieu JONARD.</p> <p>The repository contains the three following files :</p> <ul> <li>CalibrationResults.csv: Bayes factors and summary statistics of parameter estimates for each calibration run</li> <li>ParameterPosteriorDistributions.csv: median values and 90% credible intervals for the parameter posterior distributions</li> <li>StatisticalComparison.csv: statistics (Fractional bias, Root mean square error, Paired Student test, Pearson correlation coefficient, Parameters of the Deming regression between observed and predicted values) used to compare the 'Best model configurations'</li> </ul> <p>For more information concerning this repository or the study, please do not hesitate to contact Frédéric ANDRÉ (frederic.andre@uclouvain.be) or Mathieu JONARD (mathieu.jonard@uclouvain.be).</p>
A dataset of global variations in directional solar radiation exposure for ocular research using the libRadtran radiative transfer model
<p>Directional solar photon flux density has particular relevance to eye disease research (keratitis, cataract formation, macula degeneration) because ocular components (cornea, lens, retina) experience different exposures dependent on global location, structural geometry of the eye and human behaviour (Sliney, 1997). The human macula has a field of view of ~17<strong>°</strong>, or 0.06901537 sr (Strasburger, Rentschler & Jüttner, 2011) and its cone of exposure can be modelled at a range of global locations using a radiation transfer model to estimate different directions of irradiation. This dataset provides examples of spectral radiance within the macula field of vision, calculated with the radiative transfer model libRadtran v2.0.3 (Mayer & Kylling, 2005). Three data sets are provided at different latitudes without correction for spectral ocular transmission. Unless otherwise specified, all simulations were parametrized according to local meteorological condition (altitude, pressure, temperature) and atmospheric conditions on the simulated day (aerosol optical density, water column, O<sub>3</sub> and NO<sub>2</sub> concentrations). The model was parametrized for a subject looking northward toward the ground (-15<strong>°</strong> from horizon), at a height of 170 cm above the ground.</p> <p>For each simulation, a separate file is available for each condition (latitude, time, date, see below) that includes radiance at each wavelength. Radiance values are in mW m<sup>-2</sup> nm<sup>-1</sup> sr<sup>-1</sup>.</p> <p>The technique provides future opportunity to model global exposures of different ocular components to spectral solar irradiance using information on ocular transmission, local terrain, albedo and human behaviour in order to explore their relevance in epidemiological studies of age-related eye disease.</p> <p>For each simulation, a separate file is available for each condition (latitude, time, date, see below) that includes radiance at each wavelength. Radiance values are in mW m<sup>-2</sup> nm<sup>-1</sup> sr<sup>-1</sup>.</p> <p>The technique provides future opportunity to model global exposures of different ocular components to spectral solar irradiance using information on ocular transmission, local terrain, albedo and human behaviour in order to explore their relevance in epidemiological studies of age-related eye disease.</p> <p><em>Simulation 1: </em>This data set reports the spectral radiance from 250 - 500 nm at:</p> <ul> <li>3 latitudes (61.0: Southern Finland, 50.1 Northern France, 38.0: Central Spain).</li> <li>4 dates (April 17<sup>th</sup>, July 1<sup>st</sup>, September 1<sup>st</sup>, November 6<sup>th</sup> 2019).</li> <li>24 hours.</li> <li>8 cardinal directions (every 45<strong>° </strong>from North).</li> <li>2 aerosol optical densities (0.1 and 2.5).</li> </ul> <p><em>Simulation 2: </em>This data set reports the spectral radiance from 250 - 2,500 nm at:</p> <ul> <li>3 latitudes (61.0: Southern Finland, 50.1 Northern France, 38.0: Central Spain).</li> <li>4 dates (April 17<sup>th</sup>, July 1<sup>st</sup>, September 1<sup>st</sup>, November 6<sup>th</sup> 2019).</li> <li>24 hours.</li> <li>1 cardinal direction (North).</li> <li>2 aerosol optical densities (0.1 and 2.5).</li> </ul> <p><em>Simulation 3: </em>This data set reports the spectral radiance from 250 - 500 nm at:</p> <ul> <li>1 latitude (61.0: Southern Finland).</li> <li>4 dates (April 17<sup>th</sup>, July 1<sup>st</sup>, September 1<sup>st</sup>, November 6<sup>th</sup> 2019).</li> <li>24 hours.</li> <li>9 cardinal directions (every 40<strong>° </strong>from North).</li> <li>3 bidirectional reflectance distribution functions for the ground (forest, urban, snow).</li> <li>2 tilt angles for the eye direction (0<strong>° </strong> from horizon or -15<strong>°</strong> from horizon, toward the ground).</li> </ul> <p> </p>
Transfer curve models for synthetic AHL-receiver devices
<p>The input-output function of the AHL-receiver devices was determined by fitting cell fluorescence data with the following four-parameter logistical curve model:</p> <p>GFP = b + ( a-b ) / 1 +10^( ( log(EC50)-log([AHL]) )*h)</p> <p>where <em>a</em> is the maximal GFP output, <em>b</em> is the basal GFP output, <em>[AHL]</em> is the AHL inducer concentration, <em>GFP</em> is the green fluorescence response of the device for that inducer concentration, <em>EC50</em> is the inducer concentration that results in half maximal activation of the device, and <em>h</em> is proportional to the value of the steepest slope along the curve (Hill coefficient) that indicates the responsiveness of the device to the input.</p>
Heat Transfer Physics - Flat Plate Model
<p>The dataset includes unprocessed and processed temperature evolution plots for wide range of experimental conditions corresponding to ice crystal icing performed at the icing wind tunnel of TU Braunschweig within the scope of MUSIC-haic project. In addition to temperature plots the dataset also includes information on the design and components of the test article as well as the respective test matrix. It covers wide range of parametric variation including heat flux, wet bulb temperature, flow velocity and ice water content and provides a sound basis for calibration and validation of numerical tools.</p>
Data from: Evaluating temporal and spatial transferability of a tidal inundation model for foraging waterbirds
<p>For ecosystem models to be applicable outside their context of development, temporal and spatial transferability must be demonstrated. This presents a challenge for modeling intertidal ecosystems where spatiotemporal variation arises at multiple scales. Models specializing in tidal dynamics are generally inhibited from having wider ecological applications by coarse spatiotemporal resolution or high user competency. The Tidal Inundation Model of Shallow-water Availability (TiMSA) uniquely simulates tides to empirically derive a time-integrated measure of availability for a shallow water depth range defined by the user. To evaluate temporal and spatiotemporal transferability, we employed TiMSA at the development site in the Florida Keys and at novel sub-sites in the Florida Bay (application site) under a different time period (application period). We used foraging Little Blue Herons (<em>Egretta caerulea</em>) as the ecological unit with which to constrain the model's 'water depth window', i.e., range of water depths to estimate shallow-water availability. At the development site, temporally consistent water depth windows contrasted with interannual variation in shallow-water availability which revealed short-term changes in Little Blue Heron foraging habitat. At the application site, water depth accuracy varied by sub-site and was correlated with spatial error in bathymetric elevation. Although TiMSA parameters were sensitive to environmental temporal variation and uncertainty in spatial data, a spatially-explicit water depth window generated reliable estimates of shallow-water conditions over space and time at the development and application sites. By exploring the contributing factors to model error, we provide solutions to reduce uncertainty of TiMSA parameters at potential application sites and recommendations for addressing bathymetric inaccuracy in digital elevation models. Accurately quantifying spatiotemporal changes of shallow-water has implications for monitoring habitat conditions for tidally-influenced species and projecting future changes to coastal ecosystems in response to anthropogenic stressors and natural disturbances such as sea level rise.</p>
Data generated by the model presented in the research article entitled "Simulation of mass and heat transfer in an evaporatively cooled PEM fuel cell"
<p>This repository provides all the data and scripts necessary to reproduce the line plots shown in the manuscript entitled "Simulation of mass and heat transfer in an evaporatively cooled PEM fuel cell".</p>
Factors influencing transferability in species distribution models
<p>Species distribution models (SDMs) provide insights into species' ecology and distributions and are frequently used to guide conservation priorities. However, many uses of SDMs require model transferability, which refers to the degree to which a model built in one place or time can successfully predict distributions in a different place or time. If a species' model has high spatial transferability, the relationship between abundance and predictor variables should be consistent across a geographical distribution. We used Breeding Bird Surveys, climate and remote sensing data, and a novel method for quantifying model transferability to test whether SDMs can be transferred across the geographic ranges of 129 species of North American birds. We also assessed whether species' traits are correlated with model transferability. We expected that prediction accuracy between modeled regions should decrease with 1) geographical distance, 2) degree of extrapolation, and 3) were affected by a 'core-boundary' effect, which assesses distances to the boundary of a distribution. Our results suggest that very few species have a high model transferability index (<em>MTI</em>). Species with large distributions, with distributions located in areas with low topographic relief, and with short lifespans are more likely to exhibit low transferability. Transferability between modeled regions also decreased with geographical distance and degree of extrapolation. We expect that low transferability in SDMs potentially resulted from both ecological non-stationarity (i.e., biological differences within a species across its range) and over-extrapolation. Accounting for non-stationarity and extrapolation should substantially increase prediction success of species distribution models, therefore enhancing the success of conservation efforts.</p>
Equivariant analytical mapping of first principles Hamiltonians to accurate and transferable materials models
<p>Supporting data for <a href="https://arxiv.org/abs/2111.13736">https://arxiv.org/abs/2111.13736</a>.</p> <p>ACEhamiltonians.jl code</p> <p>This is an archived copy of the ACEhamiltonians.jl code to accompany the paper <a href="https://arxiv.org/abs/2111.13736">arXiv:2111.13736</a>.</p> <p>See <a href="https://github.com/ACEsuit/ACEhamiltoniansExamples">https://github.com/ACEsuit/ACEhamiltoniansExamples</a> for examples of how to use this code.</p> <p>The code is written in <a href="https://julialang.org/">Julia</a> and requires v1.6 or later. To install the Julia depenendencies:</p> <pre><code><code>$ cd ACEhamiltonians.jl $ julia julia> import Pkg julia> Pkg.activate(".") julia> Pkg.instantiate() </code></code></pre> <p>The scripts <code>test/plots.jl</code>, <code>test/fcc-to-bcc.jl</code> and <code>test/vacancy.jl</code> which produce all the plots in the paper can then run as, e.g.</p> <pre><code><code>julia --project=. test/plots.jl </code></code></pre> <p>Training data</p> <p>The <code>training_data</code> folder contains the atomic structure, Hamiltonian and overlap matrices stored in HDF5 format with the following schema:</p> <ul> <li>Data Group : <strong>aitb/</strong></li> <li>Datasets : <ul> <li><strong>H</strong> : Real-space Hamiltonian Matrix. Type: Float64. Shape: Tensor(# of TB Cells, # of Rows, # of Columns)</li> <li><strong>S</strong> : Real-space Overlap Matrix. Type: Float64. Shape: Tensor(# of TB Cells, # of Rows, # of Columns)</li> <li><strong>energy</strong> : Energy. Unit: eV. Type: Float64. Shape: Scalar</li> <li><strong>freeenergy</strong> : Free Energy. Unit: eV. Shape: Scalar</li> <li><strong>unitcell</strong> : Unit cell vectors. Type: Float64. Shape: Matrix(3,3)</li> <li><strong>positions</strong> : Atom positions. Type: Float64. Shape: Array(3)</li> <li><strong>forces</strong> : (Optional, if available) Forces. Type: Float64. Shape: Array(3)</li> <li><strong>metadata</strong> : JSON String including dictionary of information of FHIaims calculation (k-points, basis sets), TB Cells, Cutoff, Orbital definitions.,</li> </ul> </li> </ul> <p>The molecular dynamics and FHI-aims parameters are described in the manuscript.</p> <p>On-site models</p> <p>The <code>onsite_models_ord2</code> folder contains our correlation order 2 models for the on site blocks of the Hamiltonian, in a JSON format readable by the <a href="https://github.com/acesuit/ACE.jl">ACE.jl</a> and <a href="https://github.com/ACEsuit/ACEhamiltonians.jl">ACEhamiltonians.jl</a> Julia packages. There are separate files for the Hamiltonian (<code>*_H.json</code>) and overlap (<code>*_S.json</code>) models. The JSON files also contain training and test sets and associated errors as plotted in Figure 3 in our manuscript.</p> <p>Models have a unique identifier (UUID) which is a hash of the input parameters and training data. The mapping from (order, max_degree) to UUID is as follows:</p> <pre><code><code>(2,4) - 13427527590286463256 (2,5) - 10538156191357510769 (2,6) - 1646489440533135164 (2,7) - 12130775482127724115 (2,8) - 12487060958610974041 (2,9) - 2653067664384673997 (2,10) - 1143382251563115664 (2,11) - 4564001820340015372 (2,12) - 9474261500251782658 </code></code></pre> <p>Off-site models</p> <p>The <code>offsite_models_ord1</code> and <code>offsite_models_ord2</code> folders contain our order 1 and order 2 offsite models for Hamiltonian and overlap matrices. The mapping from (H_order, H_max_degree) + (S_order, S_max_degree) to UUID is as follows:</p> <pre><code><code>(1,6) + (1,8) - 7014526518680934587 (1,7) + (1,9) - 8594416159488562244 (1,8) + (1,10) - 10204186688118368371 (1,9) + (1,11) - 13078304848585360574 (1,10)+ (1,12) - 14750835312950641338 (1,11)+ (1,13) - 9883802224093245794 (1,12)+ (1,14) - 3907899412408606585 (1,13)+ (1,15) - 201683837542179657 (1,14)+ (1,16) - 277744202775070779 (2,6) + (1,8) - 4699475053563592071 (2,7) + (1,9) - 489637409713831432 (2,8) + (1,10) - 18034631670613263469 (2,9) + (1,11) - 720654516759450160 (2,10)+ (1,12) - 15214900801060024044 (2,11)+ (1,13) - 13798832597295943078 (2,12)+ (1,14) - 13162803789413134473 </code></code></pre> <p>FCC only</p> <p>Onsite models:</p> <pre><code><code>2 6 5311732756869418284 2 7 13030014632886405308 2 8 5820099621734447846 2 9 10161014511878227635 2 10 11298425190201843107 2 11 9932031839231628354 2 12 9447261873515969583 </code></code></pre> <p>Optimised FCC model <code>16110190062237887798</code></p> <p>BCC only</p> <p>Onsite models:</p> <pre><code><code>2 6 8949023800586845770 2 7 8045797268444730200 2 8 6919809282139600809 2 9 9935027806122780319 2 10 6376963380608532713 2 11 5001375576268070883 2 12 9678585765722197901 </code></code></pre> <p>Optimised BCC model <code>10293566074413000591</code></p> <p>FCC+BCC optimised models</p> <p>Onsite models</p> <pre><code><code>2 6 2154760103892646619 2 7 6450474921309693835 2 8 14227277988574899288 2 9 476820595195218567 2 10 5364136683220082110 2 11 14619519825012606580 2 12 14181614899005838824 </code></code></pre> <p>Offsite FCC+BCC optimised model - <code>4570230078043807257</code></p> <p>Model errors</p> <p>The <code>model_errors</code> directory contains summarised model errors for the training and testing errors for the models listed above.</p> <p>Reference data</p> <p>Reference electronic structure data computed for the BCC and FCC crystals, along the Bain path and for the relaxed vacancy is stored in the <code>reference_data</code> folder. The Hamiltonian and overlap matrices are stored as compressed binary HDF5 files. The format and metadata can be viewed with the <code>h5dump</code> utility, or read in using the supplied Julia code (or indeed from other languages).</p> <p>Predicted data</p> <p>The <code>predicted_data/FCC</code> and <code>predicted_data/BCC</code> folders contain HDF5 files with the results of all model predictions shown in the manuscript on the FCC and BCC crystal structures. <code>predicted_data/FCC-to-BCC</code> contains the results of predictions along the Bain path with the optimized model described in the manuscript and <code>predicted_data/vacancy</code> contains the vacancy calculations.</p>
Data & Codes used in: Quantum Mechanical Derived (VdW-DFT) Transferable Lennard-Jones and Morse Potentials to Model Cysteine and Alkanethiol Adsorption on Au(111)
<p>Here we provide the data, codes, and outline the procedure to reproduce the results presented in the paper "Quantum Mechanical Derived (VdW-DFT) Transferable Lennard-Jones and Morse Potentials to Model Cysteine and Alkanethiol Adsorption on Au(111)" by E. Ventura-Macias, P. M. Martinez, Rubén Pérez, and J. G. Vilhena.</p> <p>The following sections contain a detailed description of the data and codes. At the end of this README, you will find instructions on how to generate the classical force-field parameters (Morse and Lennard-Jones) from the potential energy surfaces (PES) computed at the DFT level.</p> <p>The procedure is general and applies to any given pair of molecule and surface. The provided codes will allow you to swiftly generate the PES at the DFT level, fit the Lennard-Jones and Morse potentials, and test them in a LAMMPS MD simulation.</p> <p>For a thorough explanation of the procedure and the relevance of these results, please refer to the original publication (ARTICLE_DOI).</p> <p>If you find this helpful, please consider citing the article (ARTICLE_DOI).</p> <h2>Data structure</h2> <p>The data is organized in the following way:</p> <ol> <li> <p>DFT</p> <ul> <li>The equilibrium adsorption geometry of methanethiol (MTH), propanethiol (PTH), and cysteine (CYS) for the Au-mol configuration with PBE+DFT-D3.</li> <li>Potential Energy Surface (PES) computed at the DFT level (Figure 3 of the main manuscript).</li> <li>The scripts used to generate the PES.</li> </ul> </li> <li> <p>MD</p> <ul> <li>Fitting code and general instructions on how to use it.</li> <li>General input scripts used to generate MD data within LAMMPS.</li> </ul> </li> </ol> <h3>DFT Data</h3> <p>The DFT data in <code>DFT.zip</code> is organized in the following way:</p> <ul> <li> <p><code>DFT_PES/</code></p> <p>This folder contains the DFT potential energy surfaces (PES) for the interaction of the sulfur atom of methanethiolate (<code>mth</code>), propanethiolate (<code>pth</code>), and cysteine (<code>cys</code>) with the Au(111) surface and the necessary scripts to reproduce it.</p> <ul> <li> <p><code>results/</code></p> <p>The PES are given in one csv file per molecule named as <em><code>mol</code></em> + <code>_PES_S-Au111.csv</code>, where <em><code>mol</code></em> is the molecule name. Columns are as follows:</p> <table> <tbody> <tr> <td><strong>Label</strong></td> <td><strong>Definition</strong></td> </tr> <tr> <td><em>i</em></td> <td>calculation number</td> </tr> <tr> <td><em>site</em></td> <td>adsorption site</td> </tr> <tr> <td><em>z</em></td> <td>distance of the S atom to the surface</td> </tr> <tr> <td><em>deltaz</em></td> <td>distance difference from the minimum energy position of the S atom</td> </tr> <tr> <td><em>pbed3</em></td> <td>PBE+D3 binding energy</td> </tr> <tr> <td><em>pbe</em></td> <td>PBE component of the binding energy</td> </tr> <tr> <td><em>d3</em></td> <td>DFT-D3 component of the binding energy</td> </tr> </tbody> </table> </li> </ul> </li> </ul> <ul> <li> <ul> <li> <p><code>mth/</code> | <code>pth/</code> | <code>cys/</code></p> <p>Each folder contains the CONTCAR (VASP) file for the optimized geometry of the molecule adsorbed on the Au(111) surface with PBE+D3.</p> </li> <li> <p><code>setup_grid.py</code></p> <p>Python script to set up the POSCAR files for the PES calculations.</p> </li> <li> <p><code>read_results.py</code></p> <p>Python script to read the results of the PES calculations.</p> </li> <li> <p><code>sub_array.sh</code></p> <p>Bash script to submit the PES calculations to an SLURM-based cluster.</p> </li> <li> <p><code>INCAR</code> | <code>KPOINTS</code> | <code>surf.CONTCAR</code></p> <p>VASP input files for the PES calculations.</p> </li> </ul> </li> </ul> <h3>MD fitting</h3> <p>The MD data in MD.zip is are organized as:</p> <ul> <li> <p><code>Fitting/</code></p> <ul> <li><code>optimize_Morse.py</code></li> </ul> <p>Contains the Python script used for the fitting procedure of Morse potential.</p> <ul> <li><code>optimize_LJ.py</code></li> </ul> <p>Contains the Python script used for the fitting procedure of LJ potential.</p> </li> <li> <p><code>Histogram/</code></p> <ul> <li><code>in.test</code></li> </ul> <p>LAMMPS input script to extract an XY file for the position of the S atom in an NVT simulation.</p> <ul> <li><code>coord.data</code></li> </ul> <p>Au surface for LAMMPS simulations.</p> <ul> <li><code>SCH3.data</code></li> </ul> <p>SCH3 molecule for LAMMPS simulations.</p> <ul> <li><code>sheng.eam</code></li> </ul> <p>EAM potential file in case Au dynamics are wished to be included.</p> </li> <li> <p><code>Single_point_scan/</code></p> <ul> <li><code>in.scan</code></li> </ul> <p>LAMMPS input script to perform single-point energy scan of a given molecule.</p> <ul> <li><code>coord.data</code></li> </ul> <p>Au surface for LAMMPS simulations.</p> <ul> <li><code>SCH3.data</code></li> </ul> <p>SCH3 molecule for LAMMPS simulations.</p> <ul> <li><code>launch.sh</code></li> </ul> <p>Launches the single point scan.</p> <ul> <li><code>plot_scan.py</code></li> </ul> </li> <li> <p><code>Molecules</code></p> <p>LAMMPS sample geometries for the 3 molecules.</p> </li> </ul> <h2>Steps to reproduce the results</h2> <p>The PES calculations were performed using the VASP code and two Python scripts for setup and results parsing.</p> <h3>Requirements</h3> <ul> <li>VASP (tested with version 5.4.4) <ul> <li><code>PAW_PBE</code> pseudopotentials set version 5.4</li> </ul> </li> <li>Python3 with packages: <ul> <li>ASE (Atomic Simulation Environment)</li> <li>Numpy</li> <li>Pandas</li> <li>matplotlib (optional)</li> </ul> </li> </ul> <h3>Steps</h3> <p>Each molecule has its own directory with the necessary files to reproduce the results. The following steps are for the methanethiolate molecule (<code>mth</code>).</p> <ol> <li>Set up the grid of points for the PES calculations by running the <code>setup_grid.py</code> script. It will create a subfolder <code>run/</code> inside the molecule's directory with the POSCAR files for each point in the grid.</li> </ol> <blockquote> <p>python setup_grid.py mth</p> </blockquote> <ol> <li> <p>Create the corresponding <code>POTCAR</code> file and place it in the molecule's directory.</p> </li> <li> <p>Change the <code>sub_array.sh</code> script to match the number of calculations in the array numbers and the MOL variable.</p> </li> </ol> <pre><code>#SBATCH --array=1-number of calculations MOL=mth</code></pre> <ol> <li>Submit the calculations to a SLURM-based cluster by running the <code>sub_array.sh</code> script from the <code>DFT_PES</code> directory.</li> </ol> <blockquote> <p>sbatch sub_array.sh</p> </blockquote> <ol> <li>After the calculations are finished, run the <code>read_results.py</code> script to parse the results and generate the PES csv files. It takes the arguments <code>--surf</code> and <code>--mol</code> to specify the surface and molecule PBE+D3 and D3 total energies.</li> </ol> <blockquote> <p>python read_results.py mth --surf -128.5228 -17.7147 --mol -22.6026 -0.0083</p> </blockquote> <h3>Reference values for the PBE+D3 and D3 surface and molecule energies</h3> <table> <tbody> <tr> <td> </td> <td><strong>Surface</strong></td> <td> </td> <td><strong>Molecule</strong></td> <td> </td> </tr> <tr> <td><strong>Molecule</strong></td> <td><strong>PBE+D3<br></strong></td> <td><strong>D3</strong></td> <td><strong>PBE+D3</strong></td> <td><strong>D3</strong></td> </tr> <tr> <td>mth</td> <td>-128.5228</td> <td>-17.7147</td> <td>-22.6026</td> <td>-0.0083</td> </tr> <tr> <td>pth</td> <td>-128.5228</td> <td>-17.7147</td> <td>-55.8615</td> <td>-0.0086</td> </tr> <tr> <td>cys</td> <td>-128.5228</td> <td>-17.7147</td> <td>-74.0338</td> <td>-0.1611</td> </tr> </tbody> </table> <h3>Fitting procedure</h3> <p>Both the .xyz and .csv files should be located at the same folder as the script. Then, simply run the code (<code>mth</code> is used as an example):</p> <blockquote> <p>python optimize_Morse.py mth</p> </blockquote> <p>or</p> <blockquote> <p>python optimize_LJ.py mth</p> </blockquote> <p>The script will print the optimized parameters: [De, re, α] or [ϵ, σ] for Morse or LJ respectively. It will also plot a fitting plot and a birdview of the resulting PES.</p> <h3>Using the potential. Histogram example</h3> <p>The code will run for the optimized <code>mth</code> Morse parameters and extract a <code>occ.lammpstrj</code> containing the (x,y) positions of the S atom throughout the NVT simulation. Note that only Au-S interaction is included. Start as:</p> <blockquote> <p>lmp -in in.test</p> </blockquote> <p>This is easily adaptable to other routines or molecules and is thought to be a generic LAMMPS starting input.</p> <h3>Single-point energy scan</h3> <p>Go to the 2C) folder and launch the scan with:</p> <blockquote> <p>./launch.sh</p> </blockquote> <p>This will create a folder named <code>fine_scan</code> containing 128 folders. Each folder is assigned to an (x,y) position. Then, inside each folder, a single-point energy evaluation is performed at various Z heights around the absolute minima.</p> <p>The <code>in.scan</code> file should be modified accordingly with the appropriate potentials. It is set to perform the scan with the optimized Morse potential by default.</p> <p>The output is gathered in the <code>E_readout.dat</code> folder with the following structure (all energies in eV):</p> <table> <tbody> <tr> <th>Total Energy</th> <th>Intramolecular energy</th> <th>Au-mol vdW interaction energy</th> <th>Au-S interaction energy</th> </tr> </tbody> <tbody> <tr> <td>-133.62</td> <td>0.123112</td> <td>-0.2403</td> <td>-1.31765</td> </tr> <tr> <td>-133.721</td> <td>0.123112</td> <td>-0.28-401</td> <td>-1.37853</td> </tr> </tbody> </table> <p>Therefore, the total adsorption energy will be the sum of the last two columns.</p> <p>Energies are ordered in increasing Z for the same (x,y) point. That is, the first 12 lines correspond to 12 heights of the starting (x,y) coordinate, the next 12 lines to heights at the second (x,y) configuration and so on.</p> <p>The python script <code>plot_scan.py</code> may be used to plot the results. The <code>E_readout.dat</code> file and <code>.csv</code> must be in the same folder.</p> <blockquote> <p>python plot_scan.py mth</p> </blockquote>
An SI-traceable protocol for the validation of radiative transfer model-based reflectance simulation: datasets
<p>This data record contains datasets used in the study "An SI-traceable protocol for the validation of radiative transfer model-based reflectance simulation":</p> <ul> <li>The <code><span>final_design.ply</span></code> file contains the mesh corresponding to the final artefact design.</li> <li>The <code><span>material_measurements.nc</span></code> file contains goniophotometer records for the material reflectance.</li> <li>The <code><span>artefact_measurements.nc</span></code> file contains goniophotometer records for the artefact reflectance.</li> </ul>
Transfer learning with generative models for object detection on limited datasets
<p>The provided datasets are used for the analysis in the work "Transfer learning with generative models for object detection on limited datasets" (https://doi.org/10.1088/2632-2153/ad65b5). The availability of data is limited in some fields, especially for object detection tasks, where it is necessary to have correctly labeled bounding boxes around each object. A notable example of such data scarcity is found in the domain of marine biology, where it is useful to develop methods to automatically detect submarine species for environmental monitoring. To address this data limitation, the state-of-the-art machine learning strategies employ two main approaches. The first involves pretraining models on existing datasets before generalizing to the specific domain of interest. The second strategy is to create synthetic datasets specifically tailored to the target domain using methods like copy-paste techniques or ad-hoc simulators. The first strategy often faces a significant domain shift, while the second demands custom solutions crafted for the specific task. In response to these challenges, here we propose a transfer learning framework that is valid for a generic scenario. In this framework, generated images help to improve the performances of an object detector in a few-real data regime. This is achieved through a diffusion-based generative model that was pretrained on large generic datasets. With respect to the state-of-the-art, we find that it is not necessary to fine tune the generative model on the specific domain of interest. We believe that this is an important advance because it mitigates the labor-intensive task of manual labeling the images in object detection tasks. We validate our approach focusing on fishes in an underwater environment, and on the more common domain of cars in an urban setting. Our method achieves detection performance comparable to models trained on thousands of images, using only a few hundreds of input data. Our results pave the way for new generative AI-based protocols for machine learning applications in various domains, for instance ranging from geophysics to biology and medicine. The provided datasets are built with the help of Gligen and the already existing NuImages, Ozfish and Deepfish datasets. The file "CarGenerated.zip" contains images generated with Gligen and with provided bounding boxes around cars in an urban environment. The file "fishes_on_bkg.zip" provides fish images generated with fishes from Deepfish inpainted with Gligen on generated backgrounds. The file "fish_text.zip" contains images completely generated with Gligen containing fishes with annotated bounding boxes. Finally, the file "oz_masked_512.zip" contains a simpler dataset of copy paste images of Deepfish fishes on Ozfish backrounds. All the files contains the images saved in different folders for training and validation, plus an index file called gt_fish.csv for the bounding boxes.</p>
Single-footprint retrievals for AIRS using a fast TwoSlab cloud-representation model and the all-sky infrared radiative transfer algorithm
<p>Dataset for AMT-2017-261 by DeSouza-Machado et. al.<br> <br> 1D-variational retrievals of temperature and moisture fields from<br> hyperspectral infrared satellite sounders use cloud-cleared radiances<br> as their observation. These derived observations allow the use of<br> clear-sky only radiative transfer in the inversion for geophysical<br> variables but at reduced spatial resolution compared to the native<br> sounder observations. Cloud-clearing can introduce various errors,<br> although scenes with large errors can be identified and<br> ignored. Information content studies show that when using multi-layer<br> cloud liquid and ice profiles in infrared hyperspectral radiative<br> transfer codes, there are typically only 2-4 degrees of freedom of<br> cloud signal. This implies a simplified cloud representation is<br> sufficient for some applications which need accurate radiative<br> transfer. Here we describe a single-footprint retrieval approach for<br> clear and cloudy conditions, which uses the thermodynamic and cloud<br> fields from Numerical Weather Prediction (NWP) models as a first<br> guess, together with a simple cloud representation model coupled to a<br> fast scattering radiative transfer algorithm (RTA). The NWP model<br> thermodynamic and cloud profiles are first co-located to the<br> observations, after which the N-level cloud profiles are<br> converted to two slab clouds (typically one for ice and one for water<br> clouds). From these, one run of our fast cloud representation model<br> allows an improvement of the \emph{a-priori} cloud state by comparing the<br> observed and model simulated radiances in the thermal window<br> channels. The retrieval yield is over 90\%, while the degrees of<br> freedom correlate with the observed window channel brightness<br> temperature which itself depends on the cloud optical depth. The cloud<br> representation/scattering package is bench-marked against radiances<br> computed using a Maximum Random Overlap cloud scheme. All-sky infrared<br> radiances measured by NASA’s Atmospheric Infrared Sounder (AIRS) and<br> NWP thermodynamic and cloud profiles from the European Center for<br> Medium Range Weather Forecasting (ECMWF) forecast model are used in<br> this paper.</p> <p> </p>
Randomly sampled coefficients for synchrotron radiative transfer in the Stokes basis, power law model, computed by rimphony, for consumption by neurosynchro
<p>This directory contains a training set of 22 million randomly-sampled radiative transfer coefficients generated by <a href="https://github.com/pkgw/rimphony/">rimphony</a>, suitable for use with the <a href="https://github.com/pkgw/neurosynchro/">neurosynchro</a> package. These coefficients can be used for numerical radiative transfer of synchrotron emission in the Stokes basis with a package such as <a href="https://github.com/jadexter/grtrans/">grtrans</a>.</p> <p>In this particular dataset, coefficients were computed using a model of a power law electron distribution isotropic in pitch angle. The input parameters, which were sampled randomly in a three-dimensional space, are:</p> <ul> <li><em>s</em>, the harmonic number, dimensionless, sampled logarithmically between 5 and 50,000,000.</li> <li><em>theta</em>, the angle between the ray path and the local magnetic field, measured in radians, sampled linearly between 0.001 and π/2 (namely, 1.5707963267948966).</li> <li><em>p</em>, the power-law index of the energetic electrons, dimensionless, sampled linearly between 1.5 and 7.</li> </ul> <p>The coefficients were computed on Harvard’s Odyssey cluster using Git commit <a href="https://github.com/pkgw/rimphony/commit/772161ebda0217b8c1ccb8ce3801ad9dc3701a4f">772161</a> of rimphony. A total of about 5,000 CPU hours were used, with 500 processes running for about 10 hours each. There are 2,748,835 data rows in total. The data are provided in their original format, split among 500 files, so that smaller subsamples of the data may be loaded easily. A README.md file provides more detailed information.</p>
Trained neural network data for synchrotron radiative transfer in the Stokes basis, power law model, computed by rimphony, for consumption by neurosynchro
<p>This archive contains data representing a trained-up neural network suitable for use with the <a href="https://github.com/pkgw/neurosynchro/">neurosynchro</a> package. The network generates coefficients that can be used for numerical radiative transfer of synchrotron emission in the Stokes basis with a package such as <a href="https://github.com/jadexter/grtrans/">grtrans</a>.</p> <p>In this particular dataset, networks were trained on a training set of coefficients generated by <a href="https://github.com/pkgw/rimphony/">rimphony</a> that is available as <a href="https://doi.org/10.5281/zenodo.1341154">DOI:10.5281/zenodo.1341154</a>. The data were generated using a model of a power law electron distribution isotropic in pitch angle. The input parameters, which were sampled randomly in a three-dimensional space, were:</p> <ul> <li><em>s</em>, the harmonic number, dimensionless, sampled logarithmically between 5 and 50,000,000.</li> <li><em>theta</em>, the angle between the ray path and the local magnetic field, measured in radians, sampled linearly between 0.001 and π/2 (namely, 1.5707963267948966).</li> <li><em>p</em>, the power-law index of the energetic electrons, dimensionless, sampled linearly between 1.5 and 7.</li> </ul> <p>The training set was computed on Harvard’s Odyssey cluster using Git commit <a href="https://github.com/pkgw/rimphony/commit/772161ebda0217b8c1ccb8ce3801ad9dc3701a4f">772161</a> of rimphony. A total of about 5,000 CPU hours were used, with 500 processes running for about 10 hours each, yielding about 22 million numbers. Training the networks took about 3 hours on an 8-core laptop.</p> <p>For the purposes of <em>neurosynchro</em>, the formats of the files in this package should be regarded as internal implementation details. The <a href="https://pypi.org/project/neurosynchro/">neurosynchro</a> Python package will load up the files in this archive and use them to predict synchrotron coefficients. For specifics, see <a href="https://neurosynchro.readthedocs.io/en/stable/">the neurosynchro documentation</a>.</p>
Transfer fine-tuned BERT models by paraphrases
<p>Transfer fine-tuned BERT models by phrasal paraphrases. </p> <ul> <li>transferFT_bert-base-uncased.pkl bases on the bert-base-uncased model</li> <li>transferFT_bert-large-uncased.pkl bases on the bert-large-uncased model</li> </ul> <p>For usage, please refer to our GitHub page.</p> <p><a href="https://github.com/yukiar/TransferFT">https://github.com/yukiar/TransferFT</a></p> <p>For details of these models, please refer to our paper.</p> <p>Yuki Arase and Junichi Tsujii. 2019. Transfer Fine-Tuning: A BERT Case Study. in Proc. of Conference on Empirical Methods in Natural Language Processing (EMNLP 2019).</p> <p><a href="https://arxiv.org/abs/1909.00931">https://arxiv.org/abs/1909.00931</a></p>
Results of Improved SMAP Soil Moisture Retrieval Using a Deep Neural Network-based Replacement of Radiative Transfer and Roughness Model
<p>This repository contains:</p> <ol> <li>A deep neural network (DNN) based soil moisture (SM) estimates (NN) based on the SMAP TB (Descending, 6 AM) and SMAP SCA-V ancillary data as the input variables. (<a href="../api/records/13309165/draft/files/SMAP_NN_36km_20150331_20220326.nc/content" target="_blank" rel="noopener noreferrer">SMAP_NN_36km_20150331_20220326.nc</a>)</li> <li>Temporally averaged roughness parameter (hNN) and scattering albedo (omegaNN) which are retrieved by inversely tracking the DNN model. (<a href="../api/records/13309165/draft/files/SMAP_hNN_omegaNN_36km_temporal_average_201503_202103.nc/content" target="_blank" rel="noopener noreferrer">SMAP_hNN_omegaNN_36km_temporal_average_201503_202103.nc</a>)</li> </ol> <p>Summary:</p> <p>The DNN model has been developed by relating SMAP TB and SMAP SCA-V ancillary data with in-situ SM data from the international soil moisture network (ISMN) using DNN. To minimize scale mismatch between gridded SMAP data and point in-situ data, the triple collocation analysis was conducted.</p> <p>The SM estimated from the DNN algorithm (NN) showed a good agreement with the ISMN data that was not used in the model training. Moreover, for a densely vegetated region located in the Amazon (Tambopata site) the NN showed less bias compared to available SM retrievals. </p> <p>Two parameters hNN and omegaNN are retrieved by ingesting NN to the modified dual channel algorithm. When the SM retrieval was conducted using the hNN and omegaNN, the result showed good agreement with the NN (DNN-based SM) with R of 0.986, ubRMSD of 0.015 m3/m3, and bias of -0.001 m3/m3.</p> <p>The paper "Improved SMAP Soil Moisture Retrieval Using a Deep Neural Network-based Replacement of Radiative Transfer and Roughness Model" published in the Transactions on Geoscience and Remote Sensing.</p> <p>For more details, please contact me (wotp12@unist.ac.kr)</p>
Data set: Modeling of Electron-Transfer Kinetics in Magnesium Electrolytes: Influence of the Solvent on the Battery Performance
<p>Dataset of the continuum simulations generated and used within the paper "<span>Modeling of Electron-Transfer Kinetics in Magnesium Electrolytes: Influence of the Solvent on the Battery Performance</span>", published in ChemSusChem (<span>2021</span><span>, </span><span>14 (21)</span><span>, 4820-4835, DOI: <span>10.1002/cssc.202101498</span></span>).</p> <p><span>The performance of rechargeable magnesium batteries is strongly dependent on the choice of electrolyte. The desolvation of multivalent cations usually goes along with high energy barriers, which can have a crucial impact on the plating reaction. This can lead to significantly higher overpotentials for magnesium deposition compared to magnesium dissolution. In this work we combine experimental measurements with DFT calculations and continuum modeling to analyze magnesium deposition in various solvents. Jointly, these methods provide a better understanding of the electrode reactions and especially the magnesium deposition mechanism. Thereby, a kinetic model for electrochemical reactions at metal electrodes is developed, which explicitly couples desolvation to electron transfer and, furthermore, qualitatively takes into account effects of the electrochemical double layer. The influence of different solvents on the battery performance is studied for<br>the state-of-the-art magnesium tetrakis(hexafluoroisopropyloxy)borate electrolyte salt. It becomes apparent that not necessarily a whole solvent molecule must be stripped from the</span> <span>solvated magnesium cation before the first reduction step can take place. For magnesium reduction it seems to be sufficient to have one coordination site available, so that the magnesium cation is able to get closer to the electrode surface. Thereby, the initial desolvation of the magnesium cation determines the deposition reaction for mono-, tri- and tetraglyme, whereas the influence of the desolvation on the plating reaction is minor for diglyme and<br>tetrahydrofuran. Overall, we can give a clear recommendation for diglyme to be applied as solvent in magnesium electrolytes</span>.<br><br></p>
Transfer learning and DNA language models enhance transcription factor binding predictions
<p>This is the dataset for replicating the results of the paper called "Transfer learning and DNA language models enhance transcription factor binding predictions" by Ekin Deniz Aksu and Martin Vingron.</p> <p>See https://github.com/ekinda/tfbs_prediction_paper</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.