def benchmark_number_of_minima():
import time, sys
import numpy as np
db = Database("test.large.db")
if True:
istart = np.random.randint(0, sys.maxint)
for i in xrange(istart, istart + 10000):
e = float(i)
db.addMinimum(e, [e], commit=False)
db.session.commit()
else:
i = 1
t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock()
t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock()
t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock()
t1 = time.clock()
e = float(i + 1)
db.addMinimum(e, [e], commit=False)
t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock()
t1 = time.clock()
print len(db.minima())
print "time", t1 - time.clock()
t1 = time.clock()
def benchmark_number_of_minima():
import time, sys
import numpy as np
db = Database("test.large.db")
if True:
istart = np.random.randint(0, sys.maxint)
for i in xrange(istart,istart+10000):
e = float(i)
db.addMinimum(e, [e], commit=False)
db.session.commit()
else:
i=1
t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock(); t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock(); t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock(); t1 = time.clock()
e = float(i+1)
db.addMinimum(e, [e], commit=False)
t1 = time.clock()
print db.number_of_minima()
print "time", t1 - time.clock(); t1 = time.clock()
print len(db.minima())
print "time", t1 - time.clock(); t1 = time.clock()
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())
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())
