def _write(self, atoms, key_value_pairs, data):
Database._write(self, atoms, key_value_pairs, data)
con = self.connection or self._connect()
self._initialize(con)
cur = con.cursor()
id = None
if not isinstance(atoms, AtomsRow):
row = AtomsRow(atoms)
row.ctime = mtime = now()
row.user = os.getenv('USER')
else:
row = atoms
cur.execute('SELECT id FROM systems WHERE unique_id=?',
(row.unique_id,))
results = cur.fetchall()
if results:
id = results[0][0]
self._delete(cur, [id], ['keys', 'text_key_values',
'number_key_values'])
mtime = now()
constraints = row._constraints
if constraints:
if isinstance(constraints, list):
constraints = encode(constraints)
else:
constraints = None
values = (row.unique_id,
row.ctime,
mtime,
row.user,
blob(row.numbers),
blob(row.positions),
blob(row.cell),
int(np.dot(row.pbc, [1, 2, 4])),
blob(row.get('initial_magmoms')),
blob(row.get('initial_charges')),
blob(row.get('masses')),
blob(row.get('tags')),
blob(row.get('momenta')),
constraints)
if 'calculator' in row:
if not isinstance(row.calculator_parameters, basestring):
row.calculator_parameters = encode(row.calculator_parameters)
values += (row.calculator,
row.calculator_parameters)
else:
values += (None, None)
if key_value_pairs is None:
key_value_pairs = row.key_value_pairs
if not data:
data = row._data
if not isinstance(data, basestring):
data = encode(data)
values += (row.get('energy'),
row.get('free_energy'),
blob(row.get('forces')),
blob(row.get('stress')),
blob(row.get('dipole')),
blob(row.get('magmoms')),
row.get('magmom'),
blob(row.get('charges')),
encode(key_value_pairs),
data,
len(row.numbers),
float_if_not_none(row.get('fmax')),
float_if_not_none(row.get('smax')),
float_if_not_none(row.get('volume')),
float(row.mass),
float(row.charge))
if id is None:
q = self.default + ', ' + ', '.join('?' * len(values))
cur.execute('INSERT INTO systems VALUES ({0})'.format(q),
values)
else:
q = ', '.join(line.split()[0].lstrip() + '=?'
for line in init_statements[0].splitlines()[2:])
cur.execute('UPDATE systems SET {0} WHERE id=?'.format(q),
values + (id,))
if id is None:
id = self.get_last_id(cur)
count = row.count_atoms()
if count:
species = [(atomic_numbers[symbol], n, id)
for symbol, n in count.items()]
cur.executemany('INSERT INTO species VALUES (?, ?, ?)',
species)
text_key_values = []
number_key_values = []
for key, value in key_value_pairs.items():
if isinstance(value, (float, int)):
number_key_values.append([key, float(value), id])
else:
assert isinstance(value, basestring)
text_key_values.append([key, value, id])
cur.executemany('INSERT INTO text_key_values VALUES (?, ?, ?)',
text_key_values)
cur.executemany('INSERT INTO number_key_values VALUES (?, ?, ?)',
number_key_values)
cur.executemany('INSERT INTO keys VALUES (?, ?)',
[(key, id) for key in key_value_pairs])
if self.connection is None:
con.commit()
con.close()
return id
