Collections

s22, dcdft, g2

class ase.collections.collection.Collection(name)[source]

Collection of atomic configurations and associated data.

Example of use:

>>> from ase.collections import s22
>>> len(s22)
22
>>> s22.names[:3]
['Ammonia_dimer', 'Water_dimer', 'Formic_acid_dimer']
>>> dimer = s22['Water_dimer']
>>> dimer.get_chemical_symbols()
['O', 'H', 'H', 'O', 'H', 'H']
>>> s22.data['Ammonia_dimer']
{'cc_energy': -0.1375}
>>> sum(len(atoms) for atoms in s22)
414

Create a collection lazily.

Will read data from json file when needed.

A collection can be iterated over to get the Atoms objects and indexed with names to get individual members.

Attributes:

name: str

Name of collection.

data: dict

Data dictionary.

filename: str

Location of json file.

names: list

Names of configurations in the collection.

S22 database of weakly interacting dimers and complexes

ase.collections.s22

S22 geometry data are from:

  1. Jurecka, J. Sponer, J. Cerny, P. Hobza; Phys Chem Chem Phys 2006, 8 (17), 1985-1993.

See http://www.begdb.com/index.php?action=106a6c241b8797f52e1e77317b96a201 for the original files. All geometries are optimized at either the CCSD(T) or MP2 level except for the methyl amide dimers where only the hydrogen position is optimized at the DFT level.

The S22 interaction energies are all calculated using both CCSD(T)/CBS counter poised corrected (CP) and MP2 /CBS CP. The original S22 interaction energies are listed in the above references. The S22 energies used here are from Takatani, T. et al., J. Chem. Phys., 132, 144104 (2010) where a large and more complete basis set has been used for all database members.

DeltaCodesDFT

ase.collections.dcdft

Structures and data from:

Lejaeghere2014

K. Lejaeghere, V. Van Speybroeck, G. Van Oost, and S. Cottenier: “Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals”, Crit. Rev. Solid State (2014). http://dx.doi.org/10.1080/10408436.2013.772503

Lejaeghere2016

Kurt Lejaeghere et al.: “Reproducibility in density functional theory calculations of solids”, Science 351 (6280), aad3000 (2016). http://dx.doi.org/10.1126/science.aad3000

This collection has WIEN2k and experimental data for:

  • volume per atom

  • bulk-modulus (in GPa)

  • pressure derivative of bulk-modulus

>>> from ase.collections import dcdft
>>> dct = dcdft.data['Cu']
>>> for key, val in sorted(dct.items()):
...     print('{:15}: {:.3f}'.format(key, val))
exp_B          : 144.279
exp_Bp         : 4.880
exp_volume     : 11.647
wien2k_B       : 141.335
wien2k_Bp      : 4.860
wien2k_volume  : 11.951

G2 neutral test set of molecules

ase.collections.g2

Molecules from [Curtiss1997].

Curtiss1997

Larry A. Curtiss, Krishnan Raghavachari, Paul C. Redfern, John A. Pople: “Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation”, J. Chem. Phys. 106, 1063 (1997). https://doi.org/10.1063/1.473182