ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
direction: string Direction for finite differences. Can be one of ‘central’ (default), ‘forward’, ‘backward’.
freq [numpy array] Optional. Can be used to create a summary on a set of known frequencies.
log [if specified, write output to a different location than] stdout. Can be an object with a write()
method or the name of a file to create.
write_jmol()
Writes file for viewing of the modes with jmol.
write_mode(n, kT=0.025852157076770025, nimages=30)
Write mode to trajectory file.
name is a string that is prefixed to the names of all the files created. atoms is an Atoms object that is either at a fully
relaxed ground state or at a saddle point. freeatoms is a list of atom indices for which the vibrational modes will
be calculated, the rest of the atoms are considered frozen. displacements is a list of displacements, one for each
free atom that are used in the finite difference method to calculate the Hessian matrix. method is -1 for backward
differences, 0 for centered differences, and 1 for forward differences.
Warning: Using the dacapo caculator you must make sure that the symmetry program in dacapo finds the
same number of symmetries for the displaced configurations in the vibrational modules as found in the ground
state used as input. This is because the wavefunction is reused from one displacement to the next. One way to
ensure this is to tell dacapo not to use symmetries.
This will show op as a python error ‘Frames are not aligned’. This could be the case for other calculators as
well.
You can get a NetCDF trajectory corresponding to a specific mode by using:
>>> mode=0
>>> vib.create_mode_trajectory(mode=mode,scaling=5)
This will create a NetCDF trajectory file CO_vib_mode_0.traj, corresponding to the highest frequency mode.
scaling is an option argument, that will give the amplitude of the mode, default is 10.
7.18 Phonon calculations
Module for calculating vibrational normal modes for periodic systems using the so-called small displacement
method (see e.g. [Alfe]). So far, space-group symmetries are not exploited to reduce the number of atomic
displacements that must be calculated and subsequent symmetrization of the force constants.
For polar materials the dynamical matrix at the zone center acquires a non-analytical contribution that accounts
for the LO-TO splitting. This contribution requires additional functionality to evaluate and is not included in the
present implementation. Its implementation in conjunction with the small displacement method is described in
[Wang].
7.19 Example
Simple example showing how to calculate the phonon dispersion for bulk aluminum using a 7x7x7 supercell
within effective medium theory:
from ase.structure import bulk
from ase.calculators.emt import EMT
from ase.dft.kpoints import ibz_points, get_bandpath
from ase.phonons import Phonons
# Setup crystal and EMT calculator
atoms = bulk(’Al’, ’fcc’, a=4.05)
calc = EMT()
7.18. Phonon calculations 147