Dataset Open Access

LDOS/SNAP data for MALA: Beryllium at 298K

Fiedler, Lenz; Cangi, Attila

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  "id": "1834", 
  "DOI": "10.14278/rodare.1834", 
  "version": "1.1.0", 
  "author": [
      "family": "Fiedler, Lenz"
      "family": "Cangi, Attila"
  "publisher": "Rodare", 
  "abstract": "<pre><em><strong>Beryllium data set for Machine Learning applications</strong></em>\f\n</pre>\f\n\f\n<p>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>\f\n-\u00a0 Gamma point (gamma_point)<br>\f\n-\u00a0 total energy convergence (k-grid converged to 1meV/atom to total energy difference, total_energy_convergence)<br>\f\n-\u00a0 LDOS convergence (k-grid converged to LDOS without unphyiscal oscillations, ldos_convergence)</p>\f\n\f\n<p>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>\f\nThe 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.</p>\f\n\f\n<pre><strong>Authors:</strong>\f\n\f\n<em>- </em>Fiedler, Lenz (HZDR / CASUS)\f\n<em>- </em>Cangi, Attila (HZDR / CASUS)\f\n\f\n<em>Affiliations</em><strong>:</strong>\f\n\f\nHZDR - Helmholtz-Zentrum Dresden-Rossendorf\f\n\f\nCASUS - Center for Advanced Systems Understanding\f\n\f\n<strong>Dataset description</strong>\f\n\f\n<em>- </em>Total size: 143G GB \f\n<em>- </em>System: Be128, Be256, Be512, Be1024, Be2048\f\n<em>- </em>Temperature(s): 298K\f\n<em>- </em>Mass density(ies): 1.896 gcc\f\n<em>- </em>Crystal Structure: hpc (material mp-87 in the materials project)\f\n<em>- </em>Number of atomic snapshots: 145\f\n  <em>  - </em>40 (Be128)\f\n  <em>  - </em>35 (Be256)\f\n   <em>- </em>30 (Be512)\f\n   <em>- </em>20 (Be1024)\f\n   <em>- </em>10 (Be2048)\f\n<em>- </em>Contents:\f\n   <em>- </em>ideal crystal structure: yes\f\n  <em>  - </em>MD trajectory: yes\f\n  <em>  - </em>Atomic positions: yes\f\n   <em>- </em>DFT inputs: yes\f\n  <em>  - </em>DFT outputs (energies): yes\f\n  <em>  - </em>SNAP vectors: yes (partially, see below)\f\n      <em>  - </em>dimensions: XxYxZx94 (last dimension: first three entries are x,y,z coordinates, data size is 91), where X, Y, Z are:\f\n         <em>- </em>Be128: 72x72x120 (size per file: 447MB)\f\n         <em>- </em>Be256: 144x72x120  (size per file: 893MB)\f\n         <em>- </em>Be512: 144x144x120 (size per file: 1.8GB)\f\n      <em>  - </em>units: a.u./Bohr\f\n  <em>  - </em>LDOS vectors: yes (partially, see below)\f\n      <em>  - </em>dimensions: XxYxZx250, where X, Y, Z are:\f\n         <em>- </em>Be128: 72x72x120 (size per file: 1.2GB)\f\n         <em>- </em>Be256: 144x72x120  (size per file: 2.4GB)\f\n         <em>- </em>Be512: 144x144x120 (size per file: 4.7GB)\f\n      <em>  - </em>units: 1/eV\f\n      <em>- </em>note: LDOS parameters are the same for all sizes of the unit cell\f\n  <em>  - </em>trained networks: no\f\n\f\n<strong>Data generation</strong>\f\n\f\nIdeal crystal structures were obtained using the Materials Project. (\f\nDFT-MD calculations were performed using either QuantumESPRESSO (, QE, for Be128, Be256 and Be512) or the Vienna Ab initio Simulation Package (, VASP, for Be1024, Be2048). DFT calculations were performed using QuantumESPRESSO. \f\nFor the VASP calculations, the standard VASP pseudopotentials were used. For Quantum Espresso, pslibrary was used (\f\nSNAP vectors were calculated using MALA ( and its LAMMPS ( interface. The LDOS was preprocessed using MALA as well.\f\n\f\n<strong>Dataset structure</strong>\f\n\f\nThe folder called \"sample_inputs\" is provided to show how MALA preprocessing and LDOS calculation have been performed. \f\nFor each temperature/mass density/number of atoms, the following subfolders exist:\f\n\f\n<em>- </em>md_inputs: Input files for the MD simulations, either as QE or VASP file(s)\f\n<em>- </em>md_outputs: The MD trajectory plus a numpy array containing the temperatures at the individual time steps\f\n<em>- </em>gamma_point\f\n<em>- </em>total_energy_convergence\f\n<em>- </em>ldos_convergence\f\n\f\nEach gamma_point/total_energy_convergence/ldos_convergence contains the following folders:\f\n\f\n<em>- </em>ldos: holds the LDOS vectors\f\n<em>- </em>fingerprints: holds the SNAP fingerprint vectors\f\n<em>- </em>snapshots: holds the atomic positions of the atomic snapshots for which DFT and LDOS calculations were performed (as .xyz files)\f\n<em>- </em>dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file\f\n<em>- </em>dft_inputs: holds the inputs for the DFT calculations, in the form of a QE input file\f\n\f\nPlease note that the numbering of the snapshots is contiguous per temperature/mass density/number of atoms, NOT within the k-grids themselves. \f\nAlso, LDOS and fingerprint files have only been calculated for snapshots in the ldos_convergence \f\nfolders. Therefore, no LDOS and fingerprint files have been calculated for the 1024 anf 2048 atom systems.\f\n</pre>", 
  "title": "LDOS/SNAP data for MALA: Beryllium at 298K", 
  "type": "dataset", 
  "issued": {
    "date-parts": [
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