Publications Repository  HelmholtzZentrum DresdenRossendorf
LDOS/SNAP data for MALA: Beryllium at 298K
Beryllium data set for Machine Learning applications
This dataset contains DFT inputs, outputs, LDOS data and fingerprint vectors for a beryllium cell at ambient conditions and varying sizes. Different levels of kgrid convergence were employed:
 Gamma point (gamma_point)
 total energy convergence (kgrid converged to 1meV/atom to total energy difference, total_energy_convergence)
 LDOS convergence (kgrid 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.
The cutoff energy was converged with respect to the energy convergence and held fixed 40Ry for all three levels of kgrids. Note that not for all sizes of unit cells data for all types of kgrid were generated.
Authors:  Fiedler, Lenz (HZDR / CASUS)  Cangi, Attila (HZDR / CASUS) Affiliations: HZDR  HelmholtzZentrum DresdenRossendorf CASUS  Center for Advanced Systems Understanding Dataset description  Total size: 143G GB  System: Be128, Be256, Be512, Be1024, Be2048  Temperature(s): 298K  Mass density(ies): 1.896 gcc  Crystal Structure: hpc (material mp87 in the materials project)  Number of atomic snapshots: 145  40 (Be128)  35 (Be256)  30 (Be512)  20 (Be1024)  10 (Be2048)  Contents:  ideal crystal structure: yes  MD trajectory: yes  Atomic positions: yes  DFT inputs: yes  DFT outputs (energies): yes  SNAP vectors: yes (partially, see below)  dimensions: XxYxZx94 (last dimension: first three entries are x,y,z coordinates, data size is 91), where X, Y, Z are:  Be128: 72x72x120 (size per file: 447MB)  Be256: 144x72x120 (size per file: 893MB)  Be512: 144x144x120 (size per file: 1.8GB)  units: a.u./Bohr  LDOS vectors: yes (partially, see below)  dimensions: XxYxZx250, where X, Y, Z are:  Be128: 72x72x120 (size per file: 1.2GB)  Be256: 144x72x120 (size per file: 2.4GB)  Be512: 144x144x120 (size per file: 4.7GB)  units: 1/eV  note: LDOS parameters are the same for all sizes of the unit cell  trained networks: no Data generation Ideal crystal structures were obtained using the Materials Project. (https://materialsproject.org/materials/mp87/) DFTMD calculations were performed using either QuantumESPRESSO (https://www.quantumespresso.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/malaproject/mala) and its LAMMPS (https://github.com/malaproject/mala) interface. The LDOS was preprocessed using MALA as well. Dataset structure 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:  md_inputs: Input files for the MD simulations, either as QE or VASP file(s)  md_outputs: The MD trajectory plus a numpy array containing the temperatures at the individual time steps  gamma_point  total_energy_convergence  ldos_convergence Each gamma_point/total_energy_convergence/ldos_convergence contains the following folders:  ldos: holds the LDOS vectors  fingerprints: holds the SNAP fingerprint vectors  snapshots: holds the atomic positions of the atomic snapshots for which DFT and LDOS calculations were performed (as .xyz files)  dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file  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 kgrids 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.

Reseach data in the HZDR data repository RODARE
Publication date: 20220218 Open access
DOI: 10.14278/rodare.1833
Versions: 10.14278/rodare.1834
License: CCBY4.0
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Permalink: https://www.hzdr.de/publications/Publ35016
Publ.Id: 35016