def create_database(self, *args, **kwargs):
"""return a new database object
See Also
--------
pele.storage
"""
kwargs = dict_copy_update(self.params["database"], kwargs)
# note this syntax is quite ugly, but we would like to be able to
# create a new database by passing the filename as the first arg,
# not as a kwarg.
if len(args) > 1:
raise ValueError(
"create_database can only take one non-keyword argument")
if len(args) == 1:
if "db" not in kwargs:
kwargs["db"] = args[0]
try:
overwrite_properties = kwargs.pop("overwrite_properties")
except KeyError:
overwrite_properties = True
# get a routine to compare the minima as exact
try:
if not "compareMinima" in kwargs:
try:
compare_minima = self.get_compare_minima()
kwargs["compareMinima"] = compare_minima
except NotImplementedError:
pass
except NotImplementedError:
# compareMinima is optional
pass
db = Database(**kwargs)
db.add_properties(self.get_system_properties(),
overwrite=overwrite_properties)
return db
def create_database(self, *args, **kwargs):
"""return a new database object
See Also
--------
pele.storage
"""
kwargs = dict_copy_update(self.params["database"], kwargs)
# note this syntax is quite ugly, but we would like to be able to
# create a new database by passing the filename as the first arg,
# not as a kwarg.
if len(args) > 1:
raise ValueError("create_database can only take one non-keyword argument")
if len(args) == 1:
if "db" not in kwargs:
kwargs["db"] = args[0]
try:
overwrite_properties = kwargs.pop("overwrite_properties")
except KeyError:
overwrite_properties = True
# get a routine to compare the minima as exact
try:
if not "compareMinima" in kwargs:
try:
compare_minima = self.get_compare_minima()
kwargs["compareMinima"] = compare_minima
except NotImplementedError:
pass
except NotImplementedError:
# compareMinima is optional
pass
db = Database(**kwargs)
db.add_properties(self.get_system_properties(), overwrite=overwrite_properties)
return db
class TestDB(unittest.TestCase):
def setUp(self):
self.db = Database()
self.nminima = 10
for i in range(self.nminima):
e = float(i)
self.db.addMinimum(e, [e])
self.nts = 3
self.db.addTransitionState(0., [0.], self.db.minima()[0], self.db.minima()[1], eigenval=0., eigenvec=[0.])
self.db.addTransitionState(0., [0.], self.db.minima()[1], self.db.minima()[2], eigenval=0., eigenvec=[0.])
self.db.addTransitionState(0., [0.], self.db.minima()[0], self.db.minima()[2], eigenval=0., eigenvec=[0.])
def test_size(self):
self.assertEqual(len(self.db.minima()), self.nminima)
def test_energy(self):
m = self.db.minima()[0]
self.assertEqual(m.energy, 0.)
def test_coords(self):
m = self.db.minima()[0]
self.assertEqual(m.coords, [0.])
def test_sizets(self):
self.assertEqual(len(self.db.transition_states()), self.nts)
def test_energyts(self):
ts = self.db.transition_states()[0]
self.assertEqual(ts.energy, 0.)
def test_coordsts(self):
ts = self.db.transition_states()[0]
self.assertEqual(ts.coords, [0.])
def test_remove_minimum(self):
m = self.db.minima()[0]
self.db.removeMinimum(m)
self.assertEqual(len(self.db.minima()), self.nminima-1)
self.assertNotIn(m, self.db.minima())
# m should have 2 minima. both of those should be gone
self.assertEqual(len(self.db.transition_states()), self.nts-2)
def test_remove_ts(self):
ts = self.db.transition_states()[0]
self.db.remove_transition_state(ts)
self.assertEqual(self.db.number_of_transition_states(), self.nts-1)
self.assertNotIn(ts, self.db.transition_states())
# m should have 2 minima. both of those should be gone
self.assertEqual(self.db.number_of_minima(), self.nminima)
def test_getTransitionState(self):
m1 = self.db.minima()[0]
m2 = self.db.minima()[1]
m3 = self.db.minima()[-1]
self.assertIsNotNone(self.db.getTransitionState(m1, m2))
self.assertIsNone(self.db.getTransitionState(m1, m3))
def test_getMinimum(self):
m = self.db.minima()[0]
self.assertEqual(m, self.db.getMinimum(m._id))
def test_minimum_adder(self):
ma = self.db.minimum_adder()
ma(101., [101.])
self.assertEqual(len(self.db.minima()), self.nminima+1)
def test_merge_minima(self):
m1 = self.db.minima()[0]
m2 = self.db.minima()[1]
self.db.mergeMinima(m1, m2)
self.assertEqual(len(self.db.minima()), self.nminima-1)
# transition states shouldn't be deleted
self.assertEqual(len(self.db.transition_states()), self.nts)
def test_number_of_minima(self):
self.assertEqual(self.nminima, self.db.number_of_minima())
def test_number_of_transition_states(self):
self.assertEqual(self.nts, self.db.number_of_transition_states())
def test_highest_energy_minimum(self):
m1 = self.db._highest_energy_minimum()
m2 = self.db.minima()[-1]
self.assertEqual(m1, m2)
def test_maximum_number_of_minima(self):
m = self.db.addMinimum(-1., [-1.], max_n_minima=self.nminima)
self.assertEqual(self.nminima, self.db.number_of_minima())
self.assertIn(m, self.db.minima())
def test_maximum_number_of_minima_largestE(self):
e = float(self.nminima + 1)
m = self.db.addMinimum(e, [e], max_n_minima=self.nminima)
self.assertEqual(self.nminima, self.db.number_of_minima())
self.assertIsNone(m)
#ensure the highest energy minimum is still in the database
mmax = self.db._highest_energy_minimum()
self.assertEqual(mmax.energy, float(self.nminima-1))
def test_maximum_number_of_minima_minima_adder(self):
ma = self.db.minimum_adder(max_n_minima=self.nminima)
m = ma(-1., [-1.])
self.assertEqual(self.nminima, self.db.number_of_minima())
self.assertIn(m, self.db.minima())
def test_getTSfromID(self):
ts = self.db.transition_states()[0]
ts1 = self.db.getTransitionStateFromID(ts._id)
self.assertEqual(ts, ts1)
def test_property(self):
# add some system properties and ensure they were added correctly
self.db.add_property("natoms", 10)
p = self.db.get_property("natoms")
self.assertEqual(p.value(), 10)
self.db.add_property("eps", 2.1)
p = self.db.get_property("eps")
self.assertEqual(p.value(), 2.1)
self.db.add_property("author", "Jake")
p = self.db.get_property("author")
self.assertEqual(p.value(), "Jake")
self.db.add_property("data", [1, 2])
p = self.db.get_property("data")
self.assertEqual(p.value(), [1, 2])
# assert that the not set values are None
p = self.db.get_property("natoms")
self.assertIsNone(p.string_value)
self.assertIsNone(p.float_value)
self.assertIsNone(p.pickle_value)
p = self.db.get_property("noprop")
self.assertIsNone(p)
props = self.db.properties(as_dict=True)
self.assertIsInstance(props, dict)
self.assertDictContainsSubset(dict(natoms=10), props)
self.assertEqual(len(props.items()), 4)
props = self.db.properties(as_dict=False)
self.assertIn(("natoms", 10), [p.item() for p in props])
self.assertEqual(len(props), 4)
def test_property_dtype(self):
# add some system properties and ensure they were added correctly
self.db.add_property("natoms", 10, dtype="int")
p = self.db.get_property("natoms")
self.assertEqual(p.value(), 10)
self.db.add_property("eps", 2.1, dtype="float")
p = self.db.get_property("eps")
self.assertEqual(p.value(), 2.1)
self.db.add_property("author", "Jake", dtype="string")
p = self.db.get_property("author")
self.assertEqual(p.value(), "Jake")
self.db.add_property("data", [1, 2], dtype="pickle")
p = self.db.get_property("data")
self.assertEqual(p.value(), [1, 2])
def test_bad_property(self):
self.db.add_property("natoms", 10, dtype="string")
p = self.db.get_property("natoms")
self.assertEqual(p.value(), "10")
def test_property_overwrite_false(self):
self.db.add_property("natoms", 10)
# overwriting with the same value should not raise error
self.db.add_property("natoms", 10, overwrite=False)
# overwriting with a different value should raise error
with self.assertRaises(RuntimeError):
self.db.add_property("natoms", 11, overwrite=False)
def test_add_properties(self):
props = dict(natoms=10, author="jake")
self.db.add_properties(props)
for name, value in props.iteritems():
p = self.db.get_property(name)
self.assertEqual(p.value(), value)
def test_load_wrong_schema(self):
current_dir = os.path.dirname(__file__)
dbname = current_dir + "/lj6_schema1.sqlite"
with self.assertRaises(IOError):
db = Database(dbname, createdb=False)
def test_load_right_schema(self):
current_dir = os.path.dirname(__file__)
dbname = current_dir + "/lj6_schema2.sqlite"
db = Database(dbname, createdb=False)
def test_invalid(self):
m = self.db.minima()[0]
self.assertFalse(m.invalid)
m.invalid = True
self.db.session.commit()
self.assertTrue(m.invalid)
# now with a ts
m = self.db.transition_states()[0]
self.assertFalse(m.invalid)
m.invalid = True
self.db.session.commit()
self.assertTrue(m.invalid)
def test_user_data(self):
m = self.db.minima()[0]
m.user_data = dict(key="value")
self.db.session.commit()
v = m.user_data["key"]
# now with a transition state
m = self.db.transition_states()[0]
m.user_data = dict(key="value")
self.db.session.commit()
v = m.user_data["key"]
class TestDB(unittest.TestCase):
def setUp(self):
self.db = Database()
self.nminima = 10
for i in range(self.nminima):
e = float(i)
self.db.addMinimum(e, [e])
self.nts = 3
self.db.addTransitionState(0., [0.],
self.db.minima()[0],
self.db.minima()[1],
eigenval=0.,
eigenvec=[0.])
self.db.addTransitionState(0., [0.],
self.db.minima()[1],
self.db.minima()[2],
eigenval=0.,
eigenvec=[0.])
self.db.addTransitionState(0., [0.],
self.db.minima()[0],
self.db.minima()[2],
eigenval=0.,
eigenvec=[0.])
def test_add_minimum(self):
# add a duplicate minimum and ensure the db doesn't change
self.db.addMinimum(0, [0])
self.assertEqual(self.db.number_of_minima(), self.nminima)
def test_size(self):
self.assertEqual(len(self.db.minima()), self.nminima)
def test_energy(self):
m = self.db.minima()[0]
self.assertEqual(m.energy, 0.)
def test_coords(self):
m = self.db.minima()[0]
self.assertEqual(m.coords, [0.])
def test_sizets(self):
self.assertEqual(len(self.db.transition_states()), self.nts)
def test_energyts(self):
ts = self.db.transition_states()[0]
self.assertEqual(ts.energy, 0.)
def test_coordsts(self):
ts = self.db.transition_states()[0]
self.assertEqual(ts.coords, [0.])
def test_remove_minimum(self):
m = self.db.minima()[0]
self.db.removeMinimum(m)
self.assertEqual(len(self.db.minima()), self.nminima - 1)
self.assertNotIn(m, self.db.minima())
# m should have 2 minima. both of those should be gone
self.assertEqual(len(self.db.transition_states()), self.nts - 2)
def test_remove_ts(self):
ts = self.db.transition_states()[0]
self.db.remove_transition_state(ts)
self.assertEqual(self.db.number_of_transition_states(), self.nts - 1)
self.assertNotIn(ts, self.db.transition_states())
# m should have 2 minima. both of those should be gone
self.assertEqual(self.db.number_of_minima(), self.nminima)
def test_getTransitionState(self):
m1 = self.db.minima()[0]
m2 = self.db.minima()[1]
m3 = self.db.minima()[-1]
self.assertIsNotNone(self.db.getTransitionState(m1, m2))
self.assertIsNone(self.db.getTransitionState(m1, m3))
def test_getMinimum(self):
m = self.db.minima()[0]
self.assertEqual(m, self.db.getMinimum(m._id))
def test_minimum_adder(self):
ma = self.db.minimum_adder()
ma(101., [101.])
self.assertEqual(len(self.db.minima()), self.nminima + 1)
def test_minimum_adder_Ecut(self):
ma = self.db.minimum_adder(Ecut=0)
n0 = self.db.number_of_minima()
ma(101., [101.])
self.assertEqual(n0, self.db.number_of_minima())
ma(-101., [-101.])
self.assertEqual(n0 + 1, self.db.number_of_minima())
def test_minimum_adder_commit_interval(self):
ma = self.db.minimum_adder(commit_interval=2)
# replace db.session.commit with a wrapper that keeps track of how
# many times it's been called
self.real_commit = self.db.session.commit
self.count = 0
def commit_wrapper():
self.count += 1
self.real_commit()
self.db.session.commit = commit_wrapper
# commit should be called for the first minimum
ma(101., [101.])
self.assertEqual(self.count, 1)
self.assertEqual(self.nminima + 1, self.db.number_of_minima())
# commit should not be called for the second minimum
ma(102., [102.])
self.assertEqual(self.count, 1)
self.assertEqual(self.nminima + 2, self.db.number_of_minima())
# yes for the third, no for the 4th
ma(103., [103.])
self.assertEqual(self.count, 2)
ma(104., [104.])
self.assertEqual(self.count, 2)
# commit should be called when minimum adder is deleted
del ma
self.assertEqual(self.count, 3)
self.assertEqual(self.nminima + 4, self.db.number_of_minima())
def test_merge_minima(self):
m1 = self.db.minima()[0]
m2 = self.db.minima()[1]
self.db.mergeMinima(m1, m2)
self.assertEqual(len(self.db.minima()), self.nminima - 1)
# transition states shouldn't be deleted
self.assertEqual(len(self.db.transition_states()), self.nts)
def test_number_of_minima(self):
self.assertEqual(self.nminima, self.db.number_of_minima())
def test_number_of_transition_states(self):
self.assertEqual(self.nts, self.db.number_of_transition_states())
def test_highest_energy_minimum(self):
m1 = self.db._highest_energy_minimum()
m2 = self.db.minima()[-1]
self.assertEqual(m1, m2)
def test_maximum_number_of_minima(self):
m = self.db.addMinimum(-1., [-1.], max_n_minima=self.nminima)
self.assertEqual(self.nminima, self.db.number_of_minima())
self.assertIn(m, self.db.minima())
def test_maximum_number_of_minima_largestE(self):
e = float(self.nminima + 1)
m = self.db.addMinimum(e, [e], max_n_minima=self.nminima)
self.assertEqual(self.nminima, self.db.number_of_minima())
self.assertIsNone(m)
#ensure the highest energy minimum is still in the database
mmax = self.db._highest_energy_minimum()
self.assertEqual(mmax.energy, float(self.nminima - 1))
def test_maximum_number_of_minima_minima_adder(self):
ma = self.db.minimum_adder(max_n_minima=self.nminima)
m = ma(-1., [-1.])
self.assertEqual(self.nminima, self.db.number_of_minima())
self.assertIn(m, self.db.minima())
def test_getTSfromID(self):
ts = self.db.transition_states()[0]
ts1 = self.db.getTransitionStateFromID(ts._id)
self.assertEqual(ts, ts1)
def test_property(self):
# add some system properties and ensure they were added correctly
self.db.add_property("natoms", 10)
p = self.db.get_property("natoms")
self.assertEqual(p.value(), 10)
self.db.add_property("eps", 2.1)
p = self.db.get_property("eps")
self.assertEqual(p.value(), 2.1)
self.db.add_property("author", "Jake")
p = self.db.get_property("author")
self.assertEqual(p.value(), "Jake")
self.db.add_property("data", [1, 2])
p = self.db.get_property("data")
self.assertEqual(p.value(), [1, 2])
# assert that the not set values are None
p = self.db.get_property("natoms")
self.assertIsNone(p.string_value)
self.assertIsNone(p.float_value)
self.assertIsNone(p.pickle_value)
p = self.db.get_property("noprop")
self.assertIsNone(p)
props = self.db.properties(as_dict=True)
self.assertIsInstance(props, dict)
self.assertDictContainsSubset(dict(natoms=10), props)
self.assertEqual(len(list(props.items())), 4)
props = self.db.properties(as_dict=False)
self.assertIn(("natoms", 10), [p.item() for p in props])
self.assertEqual(len(props), 4)
def test_property_dtype(self):
# add some system properties and ensure they were added correctly
self.db.add_property("natoms", 10, dtype="int")
p = self.db.get_property("natoms")
self.assertEqual(p.value(), 10)
self.db.add_property("eps", 2.1, dtype="float")
p = self.db.get_property("eps")
self.assertEqual(p.value(), 2.1)
self.db.add_property("author", "Jake", dtype="string")
p = self.db.get_property("author")
self.assertEqual(p.value(), "Jake")
self.db.add_property("data", [1, 2], dtype="pickle")
p = self.db.get_property("data")
self.assertEqual(p.value(), [1, 2])
def test_bad_property(self):
self.db.add_property("natoms", 10, dtype="string")
p = self.db.get_property("natoms")
self.assertEqual(p.value(), "10")
def test_property_overwrite_false(self):
self.db.add_property("natoms", 10)
# overwriting with the same value should not raise error
self.db.add_property("natoms", 10, overwrite=False)
# overwriting with a different value should raise error
with self.assertRaises(RuntimeError):
self.db.add_property("natoms", 11, overwrite=False)
def test_add_properties(self):
props = dict(natoms=10, author="jake")
self.db.add_properties(props)
for name, value in props.items():
p = self.db.get_property(name)
self.assertEqual(p.value(), value)
def test_load_wrong_schema(self):
current_dir = os.path.dirname(__file__)
dbname = current_dir + "/lj6_schema1.sqlite"
with self.assertRaises(IOError):
db = Database(dbname, createdb=False)
def test_load_right_schema(self):
current_dir = os.path.dirname(__file__)
dbname = current_dir + "/lj6_schema2.sqlite"
db = Database(dbname, createdb=False)
def test_invalid(self):
m = self.db.minima()[0]
self.assertFalse(m.invalid)
m.invalid = True
self.db.session.commit()
self.assertTrue(m.invalid)
# now with a ts
m = self.db.transition_states()[0]
self.assertFalse(m.invalid)
m.invalid = True
self.db.session.commit()
self.assertTrue(m.invalid)
def test_user_data(self):
m = self.db.minima()[0]
m.user_data = dict(key="value")
self.db.session.commit()
v = m.user_data["key"]
# now with a transition state
m = self.db.transition_states()[0]
m.user_data = dict(key="value")
self.db.session.commit()
v = m.user_data["key"]
