DOI: 10.14278/rodare.1833
title: LDOS/SNAP data for MALA: Beryllium at 298K

description: <pre><em><strong>Beryllium data set for Machine Learning applications</strong></em> </pre> This dataset contains DFT inputs, outputs, LDOS data and fingerprint vectors for a beryllium cell at ambient conditions and varying sizes. Different levels of k-grid convergence were employed:<br> - Gamma point (gamma_point)<br> - total energy convergence (k-grid converged to 1meV/atom to total energy difference, total_energy_convergence)<br> - LDOS convergence (k-grid converged to LDOS without unphyiscal oscillations, ldos_convergence) The data set contains a .zip file for each system size (see below), as well as one .zip file containing sample scripts for recalculation and preprocessing of data.<br> The cutoff energy was converged with respect to the energy convergence and held fixed 40Ry for all three levels of k-grids. Note that not for all sizes of unit cells data for all types of k-grid were generated. <pre><strong>Authors:</strong> <em>- </em>Fiedler, Lenz (HZDR / CASUS) <em>- </em>Cangi, Attila (HZDR / CASUS) <em>Affiliations</em><strong>:</strong> HZDR - Helmholtz-Zentrum Dresden-Rossendorf CASUS - Center for Advanced Systems Understanding <strong>Dataset description</strong> <em>- </em>Total size: 143G GB <em>- </em>System: Be128, Be256, Be512, Be1024, Be2048 <em>- </em>Temperature(s): 298K <em>- </em>Mass density(ies): 1.896 gcc <em>- </em>Crystal Structure: hpc (material mp-87 in the materials project) <em>- </em>Number of atomic snapshots: 145 <em> - </em>40 (Be128) <em> - </em>35 (Be256) <em>- </em>30 (Be512) <em>- </em>20 (Be1024) <em>- </em>10 (Be2048) <em>- </em>Contents: <em>- </em>ideal crystal structure: yes <em> - </em>MD trajectory: yes <em> - </em>Atomic positions: yes <em>- </em>DFT inputs: yes <em> - </em>DFT outputs (energies): yes <em> - </em>SNAP vectors: yes (partially, see below) <em> - </em>dimensions: XxYxZx94 (last dimension: first three entries are x,y,z coordinates, data size is 91), where X, Y, Z are: <em>- </em>Be128: 72x72x120 (size per file: 447MB) <em>- </em>Be256: 144x72x120 (size per file: 893MB) <em>- </em>Be512: 144x144x120 (size per file: 1.8GB) <em> - </em>units: a.u./Bohr <em> - </em>LDOS vectors: yes (partially, see below) <em> - </em>dimensions: XxYxZx250, where X, Y, Z are: <em>- </em>Be128: 72x72x120 (size per file: 1.2GB) <em>- </em>Be256: 144x72x120 (size per file: 2.4GB) <em>- </em>Be512: 144x144x120 (size per file: 4.7GB) <em> - </em>units: 1/eV <em>- </em>note: LDOS parameters are the same for all sizes of the unit cell <em> - </em>trained networks: no <strong>Data generation</strong> Ideal crystal structures were obtained using the Materials Project. (https://materialsproject.org/materials/mp-87/) DFT-MD calculations were performed using either QuantumESPRESSO (https://www.quantum-espresso.org/, QE, for Be128, Be256 and Be512) or the Vienna Ab initio Simulation Package (https://www.vasp.at/, VASP, for Be1024, Be2048). DFT calculations were performed using QuantumESPRESSO. For the VASP calculations, the standard VASP pseudopotentials were used. For Quantum Espresso, pslibrary was used (https://dalcorso.github.io/pslibrary/). SNAP vectors were calculated using MALA (https://github.com/mala-project/mala) and its LAMMPS (https://github.com/mala-project/mala) interface. The LDOS was preprocessed using MALA as well. <strong>Dataset structure</strong> The folder called "sample_inputs" is provided to show how MALA preprocessing and LDOS calculation have been performed. For each temperature/mass density/number of atoms, the following subfolders exist: <em>- </em>md_inputs: Input files for the MD simulations, either as QE or VASP file(s) <em>- </em>md_outputs: The MD trajectory plus a numpy array containing the temperatures at the individual time steps <em>- </em>gamma_point <em>- </em>total_energy_convergence <em>- </em>ldos_convergence Each gamma_point/total_energy_convergence/ldos_convergence contains the following folders: <em>- </em>ldos: holds the LDOS vectors <em>- </em>fingerprints: holds the SNAP fingerprint vectors <em>- </em>snapshots: holds the atomic positions of the atomic snapshots for which DFT and LDOS calculations were performed (as .xyz files) <em>- </em>dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file <em>- </em>dft_inputs: holds the inputs for the DFT calculations, in the form of a QE input file Please note that the numbering of the snapshots is contiguous per temperature/mass density/number of atoms, NOT within the k-grids themselves. Also, LDOS and fingerprint files have only been calculated for snapshots in the ldos_convergence folders. Therefore, no LDOS and fingerprint files have been calculated for the 1024 anf 2048 atom systems. </pre>