def setUpClass(cls):
logging.basicConfig(level=logging.INFO)
url = 'mongodb://localhost'
abcd = ABCD.from_url(url)
abcd.print_info()
cls.abcd = abcd
def wrapper(*args, config, **kwargs):
url = config.get('url', None)
if url is None:
print('Please use abcd login first!')
exit(1)
db = ABCD.from_url(url=url)
# TODO: AST.from_string() ?!
# TODO: parser should accept list
# TODO: better ast optimisation
query_list = []
for q in kwargs.pop('default_query', []):
query_list.append(parser(q))
for q in kwargs.pop('query', []):
query_list.append(parser(q))
if not query_list:
query = None
elif len(query_list) == 1:
query = query_list[0]
else:
query = ('AND', *query_list)
func(*args, db=db, query=query, **kwargs)
def login(*, config, name, url, **kwargs):
logger.info('login args: \nconfig:{}, name:{}, url:{}, kwargs:{}'.format(
config, name, url, kwargs))
from abcd import ABCD
db = ABCD.from_url(url=url)
info = db.info()
config['url'] = url
config.save()
print('Successfully connected to the database!')
print(" type: {type}\n"
" hostname: {host}\n"
" port: {port}\n"
" database: {db}\n"
" # of confs: {number of confs}".format(**info))
import numpy as np
from collections import Counter
from abcd import ABCD
if __name__ == '__main__':
abcd = ABCD(url='mongodb://localhost:27017')
print(abcd)
abcd.print_info()
from ase.io import iread, read
from abcd import ABCD
if __name__ == '__main__':
# http requests
# url = 'http://*****:*****@localhost:27018/?authSource=admin'
# Mongoengine
# https://stackoverflow.com/questions/36200288/mongolab-pymongo-connection-error
url = 'mongodb://*****:*****@localhost:27018/?authSource=admin'
abcd = ABCD(url, db='abcd', collection='default')
print(abcd)
abcd.print_info()
with abcd as db:
db.destroy()
abcd.destroy()
direcotry = Path('../tutorials/data/')
file = direcotry / 'bcc_bulk_54_expanded_2_high.xyz'
# file = direcotry / 'GAP_6.xyz'
traj = read(file.as_posix(), index=slice(None))
abcd.print_info()
import sys
from pathlib import Path
sys.path.append('..')
from abcd import ABCD
from utils.ext_xyz import XYZReader
if __name__ == '__main__':
url = 'mongodb://localhost:27017'
abcd = ABCD(url)
for file in Path('GB_alphaFe_001/tilt/').glob('*.xyz'):
print(file)
gb_params = {
'name': 'alphaFe',
'type': 'tilt',
'params': file.name[:-4]
}
with abcd as db, XYZReader(file) as reader:
db.push(reader.read_atoms(), extra_info={'GB_params': gb_params})