Dataset Open Access

LDOS/SNAP data for MALA: Beryllium at 298K

Fiedler, Lenz; Cangi, Attila

DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="" xmlns="" xsi:schemaLocation="">
  <identifier identifierType="DOI">10.14278/rodare.1834</identifier>
      <creatorName>Fiedler, Lenz</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-8311-0613</nameIdentifier>
      <affiliation>HZDR / CASUS</affiliation>
      <creatorName>Cangi, Attila</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-9162-262X</nameIdentifier>
      <affiliation>HZDR / CASUS</affiliation>
    <title>LDOS/SNAP data for MALA: Beryllium at 298K</title>
    <date dateType="Issued">2022-02-18</date>
  <resourceType resourceTypeGeneral="Dataset"/>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo"></relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.14278/rodare.1833</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf"></relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <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;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;em&gt;- &lt;/em&gt;Fiedler, Lenz (HZDR / CASUS)
&lt;em&gt;- &lt;/em&gt;Cangi, Attila (HZDR / CASUS)


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. (
DFT-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. 
For the VASP calculations, the standard VASP pseudopotentials were used. For Quantum Espresso, pslibrary was used (
SNAP vectors were calculated using MALA ( and its LAMMPS ( 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.
All versions This version
Views 800800
Downloads 2,1312,131
Data volume 50.9 TB50.9 TB
Unique views 213213
Unique downloads 6161


Cite as