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import ase.db
from ase.io.formats import string2index
def read_db(filename, index, **kwargs):
with ase.db.connect(filename, serial=True, **kwargs) as db:
if isinstance(index, str):
try:
index = string2index(index)
except ValueError:
pass
if isinstance(index, int):
index = slice(index, index + 1 or None)
if isinstance(index, str):
# index is a database query string:
for row in db.select(index):
yield row.toatoms()
else:
start, stop, step = index.indices(db.count())
if start == stop:
return
assert step == 1
for row in db.select(offset=start, limit=stop - start):
yield row.toatoms()
def write_db(filename, images, append=False, **kwargs):
with ase.db.connect(filename, serial=True, append=append, **kwargs) as con:
for atoms in images:
con.write(atoms)
read_json = read_db
write_json = write_db
read_postgresql = read_db
write_postgresql = write_db
read_mysql = read_db
write_mysql = write_db
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