本文整理汇总了Python中pele.storage.Database.number_of_transition_states方法的典型用法代码示例。如果您正苦于以下问题：Python Database.number_of_transition_states方法的具体用法？Python Database.number_of_transition_states怎么用？Python Database.number_of_transition_states使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pele.storage.Database的用法示例。
在下文中一共展示了Database.number_of_transition_states方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test1
# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import number_of_transition_states [as 别名]
def test1(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin=os.path.join(current_dir, "points.min"),
pointsts=os.path.join(current_dir, "points.ts"),
endianness="<")
converter.convert()
self.assertEqual(db.number_of_minima(), 2)
self.assertEqual(db.number_of_transition_states(), 1)
ts = db.transition_states()[0]
self.assertAlmostEqual(ts.coords[0], 1.548324, 5)
self.assertAlmostEqual(ts.coords[2], 0.18178001, 5)
self.assertAlmostEqual(ts.coords[-1], -0.50953229, 5)
self.assertEqual((180,), ts.coords.shape)
m = db.minima()[0]
print(repr(m.coords))
self.assertAlmostEqual(m.coords[0], 1.53700142, 5)
self.assertAlmostEqual(m.coords[2], 0.87783657, 5)
self.assertAlmostEqual(m.coords[-1], -0.50953229, 5)
self.assertEqual((180,), m.coords.shape)示例2: TestDB
# 需要导入模块: from pele.storage import Database [as 别名]
# 或者: from pele.storage.Database import number_of_transition_states [as 别名]
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)
#.........这里部分代码省略.........