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bulk_vacancy.py
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bulk_vacancy.py
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#!/usr/bin/env python
# calculating vacancy formation energy for the bulk metal oxides
from pathlib import Path
import os
## parameter definition
# energy of an oxygen atom
e_oxygen = -9.85858254518912/2.0
# check if the calculation is finished
with open ('OUTCAR', 'r')as f:
if 'CPU' in f.read():
f.seek(0)
bulk_energy = float([line.split()[-1] for line in f if 'entropy=' in line][-1])
else:
print('Bulk calculation still running')
exit()
#print('Bulk energy: {}'.format(bulk_energy))
num_vacancy = len([i for i in os.listdir('.') if os.path.isdir(i)])
for i in range(1, num_vacancy+1):
dir= 'vacancy_'+ str(i)+'/OUTCAR'
if os.path.exists(dir):
with open (dir, 'r') as f:
if 'CPU' in f.read():
f.seek(0)
vacancy_energy = float([line.split()[-1] for line in f if 'entropy=' in line][-1])
vac_form_energy = vacancy_energy + e_oxygen - bulk_energy
print('Vacancy energy {}: {} and formation energy: {}'.format(i, vacancy_energy, vac_form_energy))
else:
print('Vacancy {} is still running'.format(i))
f.seek(0)
vacancy_energy = float([line.split()[-1] for line in f if 'entropy=' in line][-1])
vac_form_energy = vacancy_energy + e_oxygen - bulk_energy
print('Vacancy energy {}: {} and formation energy: {}'.format(i, vacancy_energy, vac_form_energy))