Predicting Properties of Periodic Systems from Cluster Data: A Case Study of Liquid Water

•  Description

The 1520 water clusters were extracted from Ref. 1. The respective energies and atomic forces were recomputed at the revPBE-D3/def2-TZVP [2-6], B3LYP-D3/def2-TZVP [4-6, 7, 8], and  BLYP-D3/def2-TZVP [4-6, 7, 9] level.

•  Format

The data is stored in python compressed array format (.npz) with the atomization energy in kcal/mol and atomic forces in kcal/mol/Ang. The data set contains five np.ndarray

import numpy as np
data = np.load('revpbe.npz')
data['R']   # Cartesian coordinates of nuclei in Ang.
data['E']   # Total energy in kcal/mol
data['F']   # Atomic forces in kcal/mol/Ang.
data['N']   # Number of atoms in each structure
data['Z']   # Nuclear charges

References

[1] Molpeceres G., Zaverkin V., and Kästner J., “Neural-network assisted study of nitrogen atom dynamics on amorphous solid water – I. adsorption and desorption,” Mon. Not. R. Astron. Soc. 499, 1373 (2020).

[2] P. E. Blöchl, “Projector augmented-wave method,” Phys. Rev. B 50, 17953 (1994).

[3] Y. Zhang and W. Yang, “Comment on “generalized gradient approximation made simple”,” Phys. Rev. Lett. 80, 890 (1998).

[4] S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, “A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu,” J. Chem. Phys. 132, 154104 (2010).

[5] F. Weigend and R. Ahlrichs, “Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy,” Phys. Chem. Chem. Phys. 7, 3297 (2005).

[6] F. Weigend, “Accurate Coulomb-fitting basis sets for H to Rn,” Phys. Chem. Chem. Phys. 8, 1057 (2006).

[7] A. D. Becke, “Density-functional thermochemistry. iii. the role of exact exchange,” J. Chem. Phys. 98, 5648 (1993).

[8] P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, “Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields,” J. Phys. Chem. 98, 11623 (1994).

[9] C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B 37, 785 (1988).