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())