Dataset Open Access

LDOS/SNAP data for MALA: Beryllium at 298K

Fiedler, Lenz; Cangi, Attila


JSON Export

{
  "conceptrecid": "1833", 
  "files": [
    {
      "type": "zip", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/N1024.zip"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 214946397, 
      "key": "N1024.zip", 
      "checksum": "md5:cfb934835556ca8d77cf18821b468971"
    }, 
    {
      "type": "zip", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/N128.zip"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 29186428750, 
      "key": "N128.zip", 
      "checksum": "md5:54e49d566ef88d7897e74aaf1f7138b6"
    }, 
    {
      "type": "zip", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/N2048.zip"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 112066694, 
      "key": "N2048.zip", 
      "checksum": "md5:276663b3392d2b4e035af8e6c9264ed7"
    }, 
    {
      "type": "zip", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/N256.zip"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 43680626268, 
      "key": "N256.zip", 
      "checksum": "md5:e8698b13beb3dbfbbe99f3dc35a4dd3d"
    }, 
    {
      "type": "zip", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/N512.zip"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 46934764110, 
      "key": "N512.zip", 
      "checksum": "md5:5848cbc3a3ccc52ac07a00aab525c851"
    }, 
    {
      "type": "md", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/README.md"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 4310, 
      "key": "README.md", 
      "checksum": "md5:5eb3423b53f6e223deda06eacbf13cfd"
    }, 
    {
      "type": "zip", 
      "links": {
        "self": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146/sample_inputs.zip"
      }, 
      "bucket": "e140fc44-542f-4836-8fc8-7fadcd9fd146", 
      "size": 2067, 
      "key": "sample_inputs.zip", 
      "checksum": "md5:7882af49ea82d1c715f954e8eb9e42a1"
    }
  ], 
  "stats": {
    "volume": 134470742313715.0, 
    "unique_downloads": 309.0, 
    "version_unique_downloads": 309.0, 
    "unique_views": 607.0, 
    "downloads": 5418.0, 
    "version_unique_views": 607.0, 
    "version_views": 1563.0, 
    "version_downloads": 5418.0, 
    "version_volume": 134470742313715.0, 
    "views": 1563.0
  }, 
  "owners": [
    354
  ], 
  "links": {
    "badge": "https://rodare.hzdr.de/badge/doi/10.14278/rodare.1834.svg", 
    "doi": "https://doi.org/10.14278/rodare.1834", 
    "conceptbadge": "https://rodare.hzdr.de/badge/doi/10.14278/rodare.1833.svg", 
    "conceptdoi": "https://doi.org/10.14278/rodare.1833", 
    "bucket": "https://rodare.hzdr.de/api/files/e140fc44-542f-4836-8fc8-7fadcd9fd146", 
    "html": "https://rodare.hzdr.de/record/1834", 
    "latest": "https://rodare.hzdr.de/api/records/1834", 
    "latest_html": "https://rodare.hzdr.de/record/1834"
  }, 
  "created": "2022-08-11T11:40:01.505420+00:00", 
  "id": 1834, 
  "doi": "10.14278/rodare.1834", 
  "revision": 9, 
  "conceptdoi": "10.14278/rodare.1833", 
  "metadata": {
    "description": "<pre><em><strong>Beryllium data set for Machine Learning applications</strong></em>\n</pre>\n\n<p> </p>\n\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>\n -&nbsp; Gamma point (gamma_point)<br>\n -&nbsp; total energy convergence (k-grid converged to 1meV/atom to total energy difference, total_energy_convergence)<br>\n -&nbsp; LDOS convergence (k-grid converged to LDOS without unphyiscal oscillations, ldos_convergence)</p>\n\n<p> </p>\n\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>\n 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.</p>\n\n<p> </p>\n\n<pre><strong>Authors:</strong>\n\n<em>- </em>Fiedler, Lenz (HZDR / CASUS)\n<em>- </em>Cangi, Attila (HZDR / CASUS)\n\n<em>Affiliations</em><strong>:</strong>\n\nHZDR - Helmholtz-Zentrum Dresden-Rossendorf\n\nCASUS - Center for Advanced Systems Understanding\n\n<strong>Dataset description</strong>\n\n<em>- </em>Total size: 143G GB \n<em>- </em>System: Be128, Be256, Be512, Be1024, Be2048\n<em>- </em>Temperature(s): 298K\n<em>- </em>Mass density(ies): 1.896 gcc\n<em>- </em>Crystal Structure: hpc (material mp-87 in the materials project)\n<em>- </em>Number of atomic snapshots: 145\n  <em>  - </em>40 (Be128)\n  <em>  - </em>35 (Be256)\n   <em>- </em>30 (Be512)\n   <em>- </em>20 (Be1024)\n   <em>- </em>10 (Be2048)\n<em>- </em>Contents:\n   <em>- </em>ideal crystal structure: yes\n  <em>  - </em>MD trajectory: yes\n  <em>  - </em>Atomic positions: yes\n   <em>- </em>DFT inputs: yes\n  <em>  - </em>DFT outputs (energies): yes\n  <em>  - </em>SNAP vectors: yes (partially, see below)\n      <em>  - </em>dimensions: XxYxZx94 (last dimension: first three entries are x,y,z coordinates, data size is 91), where X, Y, Z are:\n         <em>- </em>Be128: 72x72x120 (size per file: 447MB)\n         <em>- </em>Be256: 144x72x120  (size per file: 893MB)\n         <em>- </em>Be512: 144x144x120 (size per file: 1.8GB)\n      <em>  - </em>units: a.u./Bohr\n  <em>  - </em>LDOS vectors: yes (partially, see below)\n      <em>  - </em>dimensions: XxYxZx250, where X, Y, Z are:\n         <em>- </em>Be128: 72x72x120 (size per file: 1.2GB)\n         <em>- </em>Be256: 144x72x120  (size per file: 2.4GB)\n         <em>- </em>Be512: 144x144x120 (size per file: 4.7GB)\n      <em>  - </em>units: 1/eV\n      <em>- </em>note: LDOS parameters are the same for all sizes of the unit cell\n  <em>  - </em>trained networks: no\n\n<strong>Data generation</strong>\n\nIdeal crystal structures were obtained using the Materials Project. (https://materialsproject.org/materials/mp-87/)\nDFT-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. \nFor the VASP calculations, the standard VASP pseudopotentials were used. For Quantum Espresso, pslibrary was used (https://dalcorso.github.io/pslibrary/).\nSNAP 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.\n\n<strong>Dataset structure</strong>\n\nThe folder called &quot;sample_inputs&quot; is provided to show how MALA preprocessing and LDOS calculation have been performed. \nFor each temperature/mass density/number of atoms, the following subfolders exist:\n\n<em>- </em>md_inputs: Input files for the MD simulations, either as QE or VASP file(s)\n<em>- </em>md_outputs: The MD trajectory plus a numpy array containing the temperatures at the individual time steps\n<em>- </em>gamma_point\n<em>- </em>total_energy_convergence\n<em>- </em>ldos_convergence\n\nEach gamma_point/total_energy_convergence/ldos_convergence contains the following folders:\n\n<em>- </em>ldos: holds the LDOS vectors\n<em>- </em>fingerprints: holds the SNAP fingerprint vectors\n<em>- </em>snapshots: holds the atomic positions of the atomic snapshots for which DFT and LDOS calculations were performed (as .xyz files)\n<em>- </em>dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file\n<em>- </em>dft_inputs: holds the inputs for the DFT calculations, in the form of a QE input file\n\nPlease note that the numbering of the snapshots is contiguous per temperature/mass density/number of atoms, NOT within the k-grids themselves. \nAlso, LDOS and fingerprint files have only been calculated for snapshots in the ldos_convergence \nfolders. Therefore, no LDOS and fingerprint files have been calculated for the 1024 anf 2048 atom systems.\n</pre>", 
    "resource_type": {
      "title": "Dataset", 
      "type": "dataset"
    }, 
    "communities": [
      {
        "id": "rodare"
      }
    ], 
    "doc_id": "1", 
    "related_identifiers": [
      {
        "identifier": "https://www.hzdr.de/publications/Publ-35016", 
        "scheme": "url", 
        "relation": "isIdenticalTo"
      }, 
      {
        "identifier": "10.14278/rodare.1833", 
        "scheme": "doi", 
        "relation": "isVersionOf"
      }
    ], 
    "pub_id": "35016", 
    "relations": {
      "version": [
        {
          "parent": {
            "pid_type": "recid", 
            "pid_value": "1833"
          }, 
          "count": 1, 
          "index": 0, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "1834"
          }, 
          "is_last": true
        }
      ]
    }, 
    "title": "LDOS/SNAP data for MALA: Beryllium at 298K", 
    "creators": [
      {
        "affiliation": "HZDR / CASUS", 
        "name": "Fiedler, Lenz", 
        "orcid": "0000-0002-8311-0613"
      }, 
      {
        "affiliation": "HZDR / CASUS", 
        "name": "Cangi, Attila", 
        "orcid": "0000-0001-9162-262X"
      }
    ], 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "version": "1.1.0", 
    "publication_date": "2022-02-18", 
    "access_right_category": "success", 
    "doi": "10.14278/rodare.1834", 
    "access_right": "open"
  }, 
  "updated": "2023-01-27T12:56:10.232098+00:00"
}
1,563
5,418
views
downloads
All versions This version
Views 1,5631,563
Downloads 5,4185,418
Data volume 134.5 TB134.5 TB
Unique views 607607
Unique downloads 309309

Share

Cite as