Dataset Open Access

LDOS/SNAP data for MALA: Beryllium at 298K

Fiedler, Lenz; Cangi, Attila


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  <identifier identifierType="DOI">10.14278/rodare.1834</identifier>
  <creators>
    <creator>
      <creatorName>Fiedler, Lenz</creatorName>
      <givenName>Lenz</givenName>
      <familyName>Fiedler</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8311-0613</nameIdentifier>
      <affiliation>HZDR / CASUS</affiliation>
    </creator>
    <creator>
      <creatorName>Cangi, Attila</creatorName>
      <givenName>Attila</givenName>
      <familyName>Cangi</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9162-262X</nameIdentifier>
      <affiliation>HZDR / CASUS</affiliation>
    </creator>
  </creators>
  <titles>
    <title>LDOS/SNAP data for MALA: Beryllium at 298K</title>
  </titles>
  <publisher>Rodare</publisher>
  <publicationYear>2022</publicationYear>
  <dates>
    <date dateType="Issued">2022-02-18</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
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    <alternateIdentifier alternateIdentifierType="url">https://rodare.hzdr.de/record/1834</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo">https://www.hzdr.de/publications/Publ-35016</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.14278/rodare.1833</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/rodare</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.1.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;pre&gt;&lt;em&gt;&lt;strong&gt;Beryllium data set for Machine Learning applications&lt;/strong&gt;&lt;/em&gt;
&lt;/pre&gt;

&lt;p&gt; &lt;/p&gt;

&lt;p&gt;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:&lt;br&gt;
 -&amp;nbsp; Gamma point (gamma_point)&lt;br&gt;
 -&amp;nbsp; total energy convergence (k-grid converged to 1meV/atom to total energy difference, total_energy_convergence)&lt;br&gt;
 -&amp;nbsp; LDOS convergence (k-grid converged to LDOS without unphyiscal oscillations, ldos_convergence)&lt;/p&gt;

&lt;p&gt; &lt;/p&gt;

&lt;p&gt;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.&lt;br&gt;
 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.&lt;/p&gt;

&lt;p&gt; &lt;/p&gt;

&lt;pre&gt;&lt;strong&gt;Authors:&lt;/strong&gt;

&lt;em&gt;- &lt;/em&gt;Fiedler, Lenz (HZDR / CASUS)
&lt;em&gt;- &lt;/em&gt;Cangi, Attila (HZDR / CASUS)

&lt;em&gt;Affiliations&lt;/em&gt;&lt;strong&gt;:&lt;/strong&gt;

HZDR - Helmholtz-Zentrum Dresden-Rossendorf

CASUS - Center for Advanced Systems Understanding

&lt;strong&gt;Dataset description&lt;/strong&gt;

&lt;em&gt;- &lt;/em&gt;Total size: 143G GB 
&lt;em&gt;- &lt;/em&gt;System: Be128, Be256, Be512, Be1024, Be2048
&lt;em&gt;- &lt;/em&gt;Temperature(s): 298K
&lt;em&gt;- &lt;/em&gt;Mass density(ies): 1.896 gcc
&lt;em&gt;- &lt;/em&gt;Crystal Structure: hpc (material mp-87 in the materials project)
&lt;em&gt;- &lt;/em&gt;Number of atomic snapshots: 145
  &lt;em&gt;  - &lt;/em&gt;40 (Be128)
  &lt;em&gt;  - &lt;/em&gt;35 (Be256)
   &lt;em&gt;- &lt;/em&gt;30 (Be512)
   &lt;em&gt;- &lt;/em&gt;20 (Be1024)
   &lt;em&gt;- &lt;/em&gt;10 (Be2048)
&lt;em&gt;- &lt;/em&gt;Contents:
   &lt;em&gt;- &lt;/em&gt;ideal crystal structure: yes
  &lt;em&gt;  - &lt;/em&gt;MD trajectory: yes
  &lt;em&gt;  - &lt;/em&gt;Atomic positions: yes
   &lt;em&gt;- &lt;/em&gt;DFT inputs: yes
  &lt;em&gt;  - &lt;/em&gt;DFT outputs (energies): yes
  &lt;em&gt;  - &lt;/em&gt;SNAP vectors: yes (partially, see below)
      &lt;em&gt;  - &lt;/em&gt;dimensions: XxYxZx94 (last dimension: first three entries are x,y,z coordinates, data size is 91), where X, Y, Z are:
         &lt;em&gt;- &lt;/em&gt;Be128: 72x72x120 (size per file: 447MB)
         &lt;em&gt;- &lt;/em&gt;Be256: 144x72x120  (size per file: 893MB)
         &lt;em&gt;- &lt;/em&gt;Be512: 144x144x120 (size per file: 1.8GB)
      &lt;em&gt;  - &lt;/em&gt;units: a.u./Bohr
  &lt;em&gt;  - &lt;/em&gt;LDOS vectors: yes (partially, see below)
      &lt;em&gt;  - &lt;/em&gt;dimensions: XxYxZx250, where X, Y, Z are:
         &lt;em&gt;- &lt;/em&gt;Be128: 72x72x120 (size per file: 1.2GB)
         &lt;em&gt;- &lt;/em&gt;Be256: 144x72x120  (size per file: 2.4GB)
         &lt;em&gt;- &lt;/em&gt;Be512: 144x144x120 (size per file: 4.7GB)
      &lt;em&gt;  - &lt;/em&gt;units: 1/eV
      &lt;em&gt;- &lt;/em&gt;note: LDOS parameters are the same for all sizes of the unit cell
  &lt;em&gt;  - &lt;/em&gt;trained networks: no

&lt;strong&gt;Data generation&lt;/strong&gt;

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.

&lt;strong&gt;Dataset structure&lt;/strong&gt;

The folder called &amp;quot;sample_inputs&amp;quot; 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:

&lt;em&gt;- &lt;/em&gt;md_inputs: Input files for the MD simulations, either as QE or VASP file(s)
&lt;em&gt;- &lt;/em&gt;md_outputs: The MD trajectory plus a numpy array containing the temperatures at the individual time steps
&lt;em&gt;- &lt;/em&gt;gamma_point
&lt;em&gt;- &lt;/em&gt;total_energy_convergence
&lt;em&gt;- &lt;/em&gt;ldos_convergence

Each gamma_point/total_energy_convergence/ldos_convergence contains the following folders:

&lt;em&gt;- &lt;/em&gt;ldos: holds the LDOS vectors
&lt;em&gt;- &lt;/em&gt;fingerprints: holds the SNAP fingerprint vectors
&lt;em&gt;- &lt;/em&gt;snapshots: holds the atomic positions of the atomic snapshots for which DFT and LDOS calculations were performed (as .xyz files)
&lt;em&gt;- &lt;/em&gt;dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file
&lt;em&gt;- &lt;/em&gt;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.
&lt;/pre&gt;</description>
  </descriptions>
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