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import os
import pytest
import numpy as np
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms, FixBondLength
from ase.db import connect
from ase.io import read
from ase.build import molecule
names = ['testase.json', 'testase.db', 'postgresql', 'mysql', 'mariadb']
@pytest.mark.parametrize('name', names)
def test_db2(name):
if name == 'postgresql':
pytest.importorskip('psycopg2')
if os.environ.get('POSTGRES_DB'): # gitlab-ci
name = 'postgresql://ase:ase@postgres:5432/testase'
else:
name = os.environ.get('ASE_TEST_POSTGRES_URL')
if name is None:
return
elif name == 'mysql':
pytest.importorskip('pymysql')
if os.environ.get('CI_PROJECT_DIR'): # gitlab-ci
name = 'mysql://root:ase@mysql:3306/testase_mysql'
else:
name = os.environ.get('MYSQL_DB_URL')
if name is None:
return
elif name == 'mariadb':
pytest.importorskip('pymysql')
if os.environ.get('CI_PROJECT_DIR'): # gitlab-ci
name = 'mariadb://root:ase@mariadb:3306/testase_mysql'
else:
name = os.environ.get('MYSQL_DB_URL')
if name is None:
return
c = connect(name)
print(name, c)
if 'postgres' in name or 'mysql' in name or 'mariadb' in name:
c.delete([row.id for row in c.select()])
id = c.reserve(abc=7)
c.delete([d.id for d in c.select(abc=7)])
id = c.reserve(abc=7)
assert c[id].abc == 7
a = c.get_atoms(id)
c.write(Atoms())
ch4 = molecule('CH4', calculator=EMT())
ch4.constraints = [FixAtoms(indices=[1]),
FixBondLength(0, 2)]
f1 = ch4.get_forces()
print(f1)
c.delete([d.id for d in c.select(C=1)])
chi = np.array([1 + 0.5j, 0.5])
if 'db' in name:
kvp = {'external_tables':
{'blabla': {'a': 1, 'b': 2, 'c': 3},
'lala': {'a': 0.01, 'b': 0.02, 'c': 0.0}}}
else:
kvp = {'a': 1}
id = c.write(ch4, key_value_pairs=kvp,
data={'1-butyne': 'bla-bla', 'chi': chi})
row = c.get(id)
print(row.data['1-butyne'], row.data.chi)
assert (row.data.chi == chi).all(), (row.data.chi, chi)
print(row)
assert len(c.get_atoms(C=1).constraints) == 2
f2 = c.get(C=1).forces
assert abs(f2.sum(0)).max() < 1e-14
f3 = c.get_atoms(C=1).get_forces()
assert abs(f1 - f3).max() < 1e-14
a = read(name, index='id={}'.format(id))[0]
f4 = a.get_forces()
assert abs(f1 - f4).max() < 1e-14
with pytest.raises(ValueError):
c.update(id, abc={'a': 42})
c.update(id, grr='hmm')
row = c.get(C=1)
assert row.id == id
assert (row.data.chi == chi).all()
for row in c.select(include_data=False):
assert len(row.data) == 0
with pytest.raises(ValueError):
c.write(ch4, foo=['bar', 2]) # not int, bool, float or str
with pytest.raises(ValueError):
c.write(Atoms(), pi='3.14') # number as a string
with pytest.raises(ValueError):
c.write(Atoms(), fmax=0.0) # reserved word
with pytest.raises(ValueError):
c.write(Atoms(), S=42) # chemical symbol as key
id = c.write(Atoms(),
b=np.bool_(True),
i=np.int64(42),
n=np.nan,
x=np.inf,
s='NaN2',
A=42)
row = c[id]
assert isinstance(row.b, bool)
assert isinstance(row.i, int)
assert np.isnan(row.n)
assert np.isinf(row.x)
# Make sure deleting a single key works:
id = c.write(Atoms(), key=7)
c.update(id, delete_keys=['key'])
assert 'key' not in c[id]
e = [row.get('energy') for row in c.select(sort='energy')]
assert len(e) == 5 and abs(e[0] - 1.991) < 0.0005
# Test the offset keyword
ids = [row.get('id') for row in c.select()]
offset = 2
assert next(c.select(offset=offset)).id == ids[offset]
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