Phonon calculation analysisΒΆ

[1]:

import matador
from matador.plotting import plot_spectral
import os
%matplotlib inline
import pathlib

[2]:

os.chdir(pathlib.Path(matador.__file__).parent.joinpath('../examples/run3_phonons'))

First, we can plot the phonon data directly from the output files:

[28]:

plot_spectral('completed/C-OQMD_675640-CollCode28857', phonons=True, band_reorder=False, band_colour='black')

Using config from /u/fs1/me388/.matadorrc
Displaying plot...
../../_images/notebooks_non-interactive_phonon_results_4_1.png 
[29]:

plot_spectral('completed/Si-OQMD_5714-CollCode29287', phonons=True, band_colour='black')

Using config from /u/fs1/me388/.matadorrc
Reordering bands based on local gradients...
Displaying plot...
../../_images/notebooks_non-interactive_phonon_results_5_1.png

For extra features, we can load the data into the models VibrationalDOS and VibrationalDispersion, which allows us to investigate free energies.

[5]:

from matador.scrapers import phonon2dict, phonon_dos2dict

[21]:

# first, lets plot the dispersion again
Si_model, _ = phonon2dict('completed/Si-OQMD_5714-CollCode29287.phonon', as_model=True)
Si_model.plot_dispersion()

Using config from /u/fs1/me388/.matadorrc
Reordering bands based on local gradients...
Displaying plot...
../../_images/notebooks_non-interactive_phonon_results_8_1.png 
[22]:

# now, we can load the DOS and plot it.
Si_dos_model, _ = phonon_dos2dict('completed/Si-OQMD_5714-CollCode29287.phonon_dos', as_model=True)

[23]:

Si_dos_model.plot_dos()

Using config from /u/fs1/me388/.matadorrc
Displaying plot...
../../_images/notebooks_non-interactive_phonon_results_10_1.png 
[24]:

# we can also compute and plot the free energy G(T) from the frequencies computed on the DOS grid
Si_dos_model.plot_free_energy()

Using config from /u/fs1/me388/.matadorrc

[24]:

<matplotlib.axes._subplots.AxesSubplot at 0x7fa34969f518>
../../_images/notebooks_non-interactive_phonon_results_11_2.png 
[25]:

# we can also compare all these results with the corresponding results for diamond carbon
C_model, _ = phonon2dict('completed/C-OQMD_675640-CollCode28857.phonon', as_model=True)
C_dos_model, _ = phonon_dos2dict('completed/C-OQMD_675640-CollCode28857.phonon_dos', as_model=True)

[26]:

from matador.plotting import plot_spectral
plot_spectral([C_model, Si_model], phonons=True, plot_dos=False)

Using config from /u/fs1/me388/.matadorrc
Disabling projections as mutiple seeds requested.
Reordering bands based on local gradients...
Reordering bands based on local gradients...
Displaying plot...
../../_images/notebooks_non-interactive_phonon_results_13_1.png 
[27]:

ax = C_dos_model.plot_free_energy(line_kwargs=dict(label='C'))
ax = Si_dos_model.plot_free_energy(ax=ax, line_kwargs=dict(label='Si'))

Using config from /u/fs1/me388/.matadorrc
Using config from /u/fs1/me388/.matadorrc
../../_images/notebooks_non-interactive_phonon_results_14_1.png