ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
>>> atoms = create_s22_system(sys)
>>> atoms.get_chemical_symbols()
[’N’, ’H’, ’H’, ’H’, ’N’, ’H’, ’H’, ’H’]
The coupled-cluster interaction energies for the s22 and s26 systems are retrieved like this:
>>> from ase.data.s22 import s22, get_interaction_energy_s22
>>> get_interaction_energy_s22(s22[0])
-0.1375
in units of eV. For s22 these are not the original energies, but from more recent work where the same (large) basis
set was used for all complexes, yielding more accurate coupled-cluster interaction energies.
The s22x5 database expands on the original s22 data by introducing non-equilibrium geometries for each complex
(0.9, 1.0, 1.2, 1.5, and 2.0 times original intermolecular distance). However, these calculations were done in
accordance with the methods used in the original s22 work, and so is expected to inherit the same problems with
mixed basis set sizes. Assuming the interaction energy error due to this is the same in all 5 geometries for each
complex, the default s22x5 interaction energies are therefore corrected with the energy difference between original
and newer energies at the original separation.
Example:
>>> from ase.data.s22 import *
>>> sys1 = s22[0]
>>> sys1
’Ammonia_dimer’
>>> atoms1 = create_s22_system(sys1)
>>> sys2 = s22x5[0]
>>> sys2
’Ammonia_dimer_0.9’
>>> atoms2 = create_s22_system(sys2)
>>> sys3 = s22x5[1]
>>> sys3
’Ammonia_dimer_1.0’
>>> atoms3 = create_s22_system(sys3)
>>> get_interaction_energy_s22(sys1)
-0.1375
>>> get_interaction_energy_s22(sys2)
-0.1375
>>> get_interaction_energy_s22(sys3)
-0.1375
>>> get_interaction_energy_s22x5(sys2)
-0.10549743024963291
>>> get_interaction_energy_s22x5(sys3)
-0.1375
>>> get_interaction_energy_s22x5(sys3,correct_offset=False)
-0.1362
>>> get_interaction_energy_s22x5(sys1,dist=1.0)
-0.1375
>>> get_interaction_energy_s22x5(sys1,dist=0.9)
-0.10549743024963291
>>> get_interaction_energy_s22x5(sys1,dist=0.9,correct_offset=False)
-0.1045
>>> get_number_of_dimer_atoms(sys1)
[4, 4]
>>> get_s22x5_distance(sys2)
-0.25040236345454536
>>> get_s22x5_distance(sys3)
0.0
where sys1 is an s22 complex in the original geometry, while sys2 and sys3 are two different s22x5 geometries
of the exact same complex. It is seen that the interaction energies for an s22 system and its s22x5 equivalent
(indexed ‘_1.0’) does not neccesarily match when the energy offset-correction is turned off. The last two functions
168 Chapter 7. Documentation for modules in ASE