def build_db(update='.', prefix='datas'):
user = os.getenv('USER')
print('Reading.....')
dbfile = '%s.db' % prefix
with connect(dbfile) as db:
calc = Espresso()
cwd = os.getcwd()
for dire, j, y in os.walk(update):
prefix = is_espresso(dire)
if prefix:
calc.prefix = prefix
else:
continue
print(dire)
label = dire
inputfile = dire + '/%s.pwi' % calc.prefix
calc.directory = os.path.join(cwd, dire)
calc.prefix = prefix
print(inputfile)
atoms, input_data, pseudopotentials, kpts = read_espresso_input(
inputfile)
newcalc = Espresso(label=dire,
prefix=prefix,
pseudopotentials=pseudopotentials,
input_data=input_data,
kpts=kpts)
converged, fromfile, meg0 = calc.read_convergence()
calc.results = {}
try:
calc.read_results()
atoms = calc.results['atoms']
except Exception as e:
print('=' * 30, '\n', dire, e)
# atoms.calc = newcalc
print('dire: ', dire, converged)
nid = 0
for row in db.select(label=label):
dbid = row.id
nid += 1
if nid > 0:
db.write(atoms, id=dbid, label=label, converged=meg0)
else:
db.write(atoms, label=label)
print('Finished')
def summary(updates=[], prefix='datas'):
import pandas as pd
columns = [
'label', 'atoms', 'cell', 'positions', 'energy', 'forces', 'stress'
]
file = '%s.pickle' % prefix
db = '%s.db' % prefix
if os.path.exists(file):
with open(file, 'rb') as f:
datas, df = pickle.load(f)
else:
datas = {}
df = pd.DataFrame(columns=columns)
calc = Espresso()
print('Reading.....')
for update in updates:
cwd = os.getcwd()
for i, j, y in os.walk(update):
output = is_espresso(i)
if output:
os.chdir(i)
print('dire:', i)
calc.directory = cwd + '/' + i
calc.prefix = output[0:-4]
try:
calc.results = {}
calc.read_results()
# gap, p1, p2 = bandgap(calc)
# calc.results['gap'] = gap
# t = calc.get_time()
# calc.results['time'] = t
datas[i] = calc.results
atoms = calc.results['atoms']
atoms.write(
os.path.join(calc.directory, '%s.cif' % calc.prefix))
# results = ana(i, calc)
# df.loc[len(df)] = results
except Exception as e:
print('=' * 30, '\n', i, e)
os.chdir(cwd)
with open(file, 'wb') as f:
pickle.dump([datas, df], f)
print('Finished')