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vacancy_formation_energy.py
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vacancy_formation_energy.py
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#!/usr/bin/env python
# calculate surface vacancy formation energy using simple subtraction
# scheme where vacancy calculations reside in the same directory named
# 'vacancy_1' or 'vacancy_2'
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)
surface_energy = float([line.split()[-1] for line in f if 'entropy=' in line][-1])
else:
print('Surface calculation still running')
exit()
num_vacancy = len([i for i in os.listdir('.') if os.path.isdir(i)])
#print('There are {} vacancy calculations for this surface'.format(num_vacancy))
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 - surface_energy
print('Vacancy energy {}: {} and formation energy: {}'.format(i, vacancy_energy, vac_form_energy))
else:
print('Vacancy {} is still running'.format(i))