ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
>>> from ase import Atoms
>>> from ase.calculators import EMT
>>> from ase.optimize import BFGS
>>> from ase.vibrations import Vibrations
>>> n2 = Atoms(’N2’, [(0, 0, 0), (0, 0, 1.1)],
... calculator=EMT())
>>> BFGS(n2).run(fmax=0.01)
BFGS: 0 16:01:21 0.440339 3.2518
BFGS: 1 16:01:21 0.271928 0.8211
BFGS: 2 16:01:21 0.263278 0.1994
BFGS: 3 16:01:21 0.262777 0.0088
>>> vib = Vibrations(n2)
>>> vib.run()
Writing vib.eq.pckl
Writing vib.0x-.pckl
Writing vib.0x+.pckl
Writing vib.0y-.pckl
Writing vib.0y+.pckl
Writing vib.0z-.pckl
Writing vib.0z+.pckl
Writing vib.1x-.pckl
Writing vib.1x+.pckl
Writing vib.1y-.pckl
Writing vib.1y+.pckl
Writing vib.1z-.pckl
Writing vib.1z+.pckl
>>> vib.summary()
---------------------
# meV cm^-1
---------------------
0 0.0 0.0
1 0.0 0.0
2 0.0 0.0
3 2.5 20.4
4 2.5 20.4
5 152.6 1230.8
---------------------
Zero-point energy: 0.079 eV
>>> vib.write_mode(-1) # write last mode to trajectory file
get_energies(method=’standard’, direction=’central’)
Get vibration energies in eV.
get_frequencies(method=’standard’, direction=’central’)
Get vibration frequencies in cm^-1.
run()
Run the vibration calculations.
This will calculate the forces for 6 displacements per atom +/-x, +/-y, +/-z. Only those calculations
that are not already done will be started. Be aware that an interrupted calculation may produce an
empty file (ending with .pckl), which must be deleted before restarting the job. Otherwise the forces
will not be calculated for that displacement.
Note that the calculations for the different displacements can be done simultaneously by several independent
processes. This feature relies on the existence of files and the subsequent creation of the file
in case it is not found.
summary(method=’standard’, direction=’central’, freq=None, log=)
Print a summary of the vibrational frequencies.
Parameters:
method [string] Can be ‘standard’(default) or ‘Frederiksen’.
146 Chapter 7. Documentation for modules in ASE