Calculations dataset of diatomic systems based on van der Waals density functional method

Published: 12 February 2021| Version 1 | DOI: 10.17632/yz5rrmvrgd.1
Kiyou Shibata,


This dataset provides results obtained by first-principles calculations on diatomic systems and isolated systems based on SCAN+rVV10. All diatomic systems containing atomic species from H (Z=1) to Ra (Z=88) are considered. Calculations not only for diatomic systems but also for isolated systems are uploaded for evaluating binding energy, . =========================== raw_vasp_output_files [zip files (,] These zip files contain raw output files (OUTCAR and vasprun.xml) of VASP calculations. =========================== parsed_dataset [Python pickle files (diatomic_df.pickle, isolated_df.pickle) and csv files (diatomic_df.csv, isolated_df.csv)] These files contain tables of typical physical values files obtained from the VASP calculations. The python pickle files requires python environment with pandas and pymatgen. Files "*_df.pickle" and "*_df_protocol3.pickle" contains the same data, but they were saved with python pickle protocol 5 and 3, respectively. =========================== codes [] Simple python scripts for parsing raw VASP output files and plotting heatmaps and a scatter plot.


Steps to reproduce

Diatomic systems of atom pairs containing element from H (Z=1) to Ra (Z=88), 3,916 pairs in total, are considered. In addition to the diatomic systems, isolated atom systems were also calculated for evaluating binding energy. All the first-principles DFT calculations were performed with the projector augmented wave (PAW) method using the Vienna Ab-initio Simulation Package (VASP). SCAN+ r VV10 was used as vdW-DF in the implementations of the VASP code. The exchange correlation interaction was treated by the Perdew-Burke-Ernzerhof (GGA-PBE) generalized gradient approximation. Semi-core orbital was included in valence. The selection of the PAW potential can be confirmed by potcar_symbol entry in the parsed statistical datasets or by OUTCAR files in the data record uploaded in NOMAD database. Cut-off energy of 500 eV was used as a default value for most of the isolated atoms and diatomic systems, but it was altered manually for some pairs which did not converged. Spin polarization was considered, but spin orbit interaction was not considered. The Brillouin zone was sampled with a 1×1×1 Γ-centered k-point grid. All calculations were carried out in a 15 Å cubic cell, large so that interaction between mirror atoms becomes small. Each diatomic system or 37 isolated atom was positioned at the center of the cubic cell. For diatomic systems, both atomic structure and electronic structure were relaxed. For isolated atoms, only electronic structure was relaxed. The initial interatomic distance of each diatomic system was set as the sum of covalent atomic radii and was tuned manually for pairs which does not converged. Other all detailed calculation conditions can be confirmed by checking the raw VASP output files (OUTCAR and vasprun.xml).


Tokyo Daigaku Seisan Gijutsu Kenkyujo


Density Functional Theory, Theoretical Calculation, Diatomics, Bond Dissociation Energy, Van der Waals Interactions