def do_NEB(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
mindist = system.get_mindist()
pot = system.get_potential()
m1 = db.minima()[0]
for m2 in db.minima()[1:3]:
neb = NEBDriver(pot, m1.coords, m2.coords)
neb.run()
def do_NEB(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
mindist = system.get_mindist()
pot = system.get_potential()
m1 = db.minima()[0]
for m2 in db.minima()[1:3]:
neb = NEBDriver(pot, m1.coords, m2.coords)
neb.run()
def do_ts_search(nmol=20):
from pele.transition_states import findTransitionState
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
orthogopt = system.get_orthogonalize_to_zero_eigenvectors()
for ts in db.transition_states():
coords = db.transition_states()[0].coords.copy()
coords += np.random.uniform(-.5,.5, coords.size)
print system.params.double_ended_connect.local_connect_params.tsSearchParams
findTransitionState(coords, system.get_potential(), orthogZeroEigs=orthogopt,
**system.params.double_ended_connect.local_connect_params.tsSearchParams)
class TestOTPCluster(unittest.TestCase):
def setUp(self):
np.random.seed(0)
self.nmol = 4
self.system = OTPCluster(self.nmol)
pot = self.system.get_potential()
self.db = self.system.create_database()
self.m1 = self.db.addMinimum(pot.getEnergy(_x1), _x1)
self.m2 = self.db.addMinimum(pot.getEnergy(_x2), _x2)
def test1(self):
pot = self.system.get_potential()
self.assertLess(np.linalg.norm(pot.getGradient(self.m1.coords)), .1)
self.assertLess(np.linalg.norm(pot.getGradient(self.m2.coords)), .1)
def test_basinhopping(self):
db = self.system.create_database()
bh = self.system.get_basinhopping(db)
bh.setPrinting(ostream=None)
bh.run(5)
self.assertGreaterEqual(db.number_of_minima(), 1)
def test_double_ended_connect(self):
connect = self.system.get_double_ended_connect(self.m1, self.m2,
self.db)
connect.connect()
self.assertTrue(connect.success())
path = connect.returnPath()
def test_thermodynamics(self):
get_thermodynamic_information(self.system,
self.db,
nproc=None,
recalculate=True)
self.assertIsNotNone(self.m1.fvib)
mt = self.system.get_metric_tensor(self.m1.coords)
print("metric tensor")
print(mt)
class TestOTPCluster(unittest.TestCase):
def setUp(self):
np.random.seed(0)
self.nmol = 4
self.system = OTPCluster(self.nmol)
pot = self.system.get_potential()
self.db = self.system.create_database()
self.m1 = self.db.addMinimum(pot.getEnergy(_x1), _x1)
self.m2 = self.db.addMinimum(pot.getEnergy(_x2), _x2)
def test1(self):
pot = self.system.get_potential()
self.assertLess(np.linalg.norm(pot.getGradient(self.m1.coords)), .1)
self.assertLess(np.linalg.norm(pot.getGradient(self.m2.coords)), .1)
def test_basinhopping(self):
db = self.system.create_database()
bh = self.system.get_basinhopping(db)
bh.setPrinting(ostream=None)
bh.run(5)
self.assertGreaterEqual(db.number_of_minima(), 1)
def test_double_ended_connect(self):
connect = self.system.get_double_ended_connect(self.m1, self.m2, self.db)
connect.connect()
self.assertTrue(connect.success())
path = connect.returnPath()
def test_thermodynamics(self):
get_thermodynamic_information(self.system, self.db, nproc=None, recalculate=True)
self.assertIsNotNone(self.m1.fvib)
mt = self.system.get_metric_tensor(self.m1.coords)
print("metric tensor")
print(mt)
def do_ts_search(nmol=20):
from pele.transition_states import findTransitionState
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
orthogopt = system.get_orthogonalize_to_zero_eigenvectors()
for ts in db.transition_states():
coords = db.transition_states()[0].coords.copy()
coords += np.random.uniform(-.5, .5, coords.size)
print system.params.double_ended_connect.local_connect_params.tsSearchParams
findTransitionState(coords,
system.get_potential(),
orthogZeroEigs=orthogopt,
**system.params.double_ended_connect.
local_connect_params.tsSearchParams)