def do_connect(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
m1 = db.minima()[0]
for m2 in db.minima()[1:5]:
connect = system.get_double_ended_connect(m1, m2, db, fresh_connect=True)
connect.connect()
def do_mindist(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
mindist = system.get_mindist()
m0 = db.minima()[0]
for m1 in db.minima()[1:6]:
d, x1, x2 = mindist(m0.coords, m1.coords)
print d
def do_mindist(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
mindist = system.get_mindist()
m0 = db.minima()[0]
for m1 in db.minima()[1:6]:
d, x1, x2 = mindist(m0.coords, m1.coords)
print d
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 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_connect(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
m1 = db.minima()[0]
for m2 in db.minima()[1:5]:
connect = system.get_double_ended_connect(m1,
m2,
db,
fresh_connect=True)
connect.connect()
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)
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)
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 setUp(self):
np.random.seed(0)
self.nmol = 3
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)
self.x0 = np.array([
0, 1, 2, 3, 4, 5, 6, 7, 8, 0.517892, 0.575435, 0.632979, 0.531891,
0.576215, 0.620539, 0.540562, 0.5766, 0.612637
])
from pele.angleaxis.aamindist import TransformAngleAxisCluster
self.topology = self.system.aatopology
self.transform = TransformAngleAxisCluster(self.topology)
self.p0 = np.array(range(1, 4), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
def setUp(self):
np.random.seed(0)
self.nmol = 3
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)
self.x0 = np.array([ 0, 1, 2, 3, 4, 5, 6, 7, 8,
0.517892, 0.575435, 0.632979,
0.531891, 0.576215, 0.620539,
0.540562, 0.5766, 0.612637 ])
from pele.angleaxis.aamindist import TransformAngleAxisCluster
self.topology = self.system.aatopology
self.transform = TransformAngleAxisCluster(self.topology)
self.p0 = np.array(range(1,4), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
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)
class TestRBTopologyOTP(unittest.TestCase):
def setUp(self):
np.random.seed(0)
self.nmol = 3
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)
self.x0 = np.array([
0, 1, 2, 3, 4, 5, 6, 7, 8, 0.517892, 0.575435, 0.632979, 0.531891,
0.576215, 0.620539, 0.540562, 0.5766, 0.612637
])
from pele.angleaxis.aamindist import TransformAngleAxisCluster
self.topology = self.system.aatopology
self.transform = TransformAngleAxisCluster(self.topology)
self.p0 = np.array(range(1, 4), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
def test_transform_rotate(self):
print "\ntest rotate"
x = self.x0.copy()
p = np.array(range(1, 4), dtype=float)
p /= np.linalg.norm(p)
self.transform.rotate(x, rotations.aa2mx(p))
xnewtrue = np.array([
0.48757698, 0.61588594, 2.09355038, 2.02484605, 4.76822812,
4.81289924, 3.56211511, 8.92057031, 7.53224809, 0.71469473,
1.23875927, 1.36136748, 0.72426504, 1.24674367, 1.34426835,
0.73015833, 1.25159032, 1.33345003
])
for v1, v2 in izip(x, xnewtrue):
self.assertAlmostEqual(v1, v2, 5)
def test_align_path(self):
print "\ntest align_path"
x1 = self.x0.copy()
x2 = self.x0 + 5
self.topology.align_path([x1, x2])
x2true = np.array([
5., 6., 7., 8., 9., 10., 11., 12., 13., 1.92786071, 1.94796529,
1.96807021, 1.93320298, 1.94869267, 1.96418236, 1.93645608,
1.94905155, 1.96164668
])
for v1, v2 in izip(x1, self.x0):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in izip(x2, x2true):
self.assertAlmostEqual(v1, v2, 5)
def test_cpp_zero_ev(self):
print "\ntest zeroEV cpp"
x = self.x0.copy()
zev = self.topology._zeroEV_python(x)
czev = self.topology.cpp_topology.get_zero_modes(x)
self.assertEqual(len(czev), 6)
for ev, cev in izip(zev, czev):
for v1, v2 in izip(ev, cev):
self.assertAlmostEqual(v1, v2, 5)
def test_site_distance_squared(self):
print "\ntest site distance squared"
c0 = np.zeros(3)
c1 = np.ones(3)
p0 = self.p0.copy()
p1 = p0 + 1
site = self.system.make_otp()
d2 = site.distance_squared(c0, p0, c1, p1)
d2p = _sitedist(c1 - c0, p0, p1, site.S, site.W, site.cog)
self.assertAlmostEqual(d2, 10.9548367929, 5)
def test_distance_squared(self):
print "\ntest distance squared"
x1 = self.x0.copy()
x2 = self.x0 + 1.1
d2 = self.topology.distance_squared(x1, x2)
d3 = self.topology._distance_squared_python(x1, x2)
self.assertAlmostEqual(d2, 38.9401810973, 5)
self.assertAlmostEqual(d2, d3, 5)
def test_distance_squared_grad(self):
print "\ntest distance squared grad"
x1 = self.x0.copy()
x2 = self.x0 + 1.1
grad = self.topology.distance_squared_grad(x1, x2)
g2 = self.topology._distance_squared_grad_python(x1, x2)
gtrue = np.array([
-6.6, -6.6, -6.6, -6.6, -6.6, -6.6, -6.6, -6.6, -6.6, -1.21579025,
-0.07013805, -1.2988823, -1.21331786, -0.06984532, -1.28945301,
-1.2116105, -0.06975828, -1.28362943
])
for v1, v2 in izip(grad, gtrue):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in izip(grad, g2):
self.assertAlmostEqual(v1, v2, 5)
def test_measure_align(self):
print "\ntest measure align"
x1 = self.x0.copy()
x2 = self.x0 + 5.1
x2[-1] = x1[-1] + .1
x20 = x2.copy()
measure = MeasureRigidBodyCluster(self.topology)
measure.align(x1, x2)
def get_random_rbcoords(self):
otp = OTPCluster(self.nrigid)
ret = otp.get_random_minimized_configuration(tol=100.)
return ret.coords
class TestRBTopologyOTP(unittest.TestCase):
def setUp(self):
np.random.seed(0)
self.nmol = 3
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)
self.x0 = np.array([ 0, 1, 2, 3, 4, 5, 6, 7, 8,
0.517892, 0.575435, 0.632979,
0.531891, 0.576215, 0.620539,
0.540562, 0.5766, 0.612637 ])
from pele.angleaxis.aamindist import TransformAngleAxisCluster
self.topology = self.system.aatopology
self.transform = TransformAngleAxisCluster(self.topology)
self.p0 = np.array(range(1,4), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
def test_transform_rotate(self):
print "\ntest rotate"
x = self.x0.copy()
p = np.array(range(1,4), dtype=float)
p /= np.linalg.norm(p)
self.transform.rotate(x, rotations.aa2mx(p))
xnewtrue = np.array([ 0.48757698, 0.61588594, 2.09355038, 2.02484605, 4.76822812,
4.81289924, 3.56211511, 8.92057031, 7.53224809, 0.71469473,
1.23875927, 1.36136748, 0.72426504, 1.24674367, 1.34426835,
0.73015833, 1.25159032, 1.33345003])
for v1, v2 in izip(x, xnewtrue):
self.assertAlmostEqual(v1, v2, 5)
def test_align_path(self):
print "\ntest align_path"
x1 = self.x0.copy()
x2 = self.x0 + 5
self.topology.align_path([x1, x2])
x2true = np.array([ 5. , 6. , 7. , 8. ,
9. , 10. , 11. , 12. ,
13. , 1.92786071, 1.94796529, 1.96807021,
1.93320298, 1.94869267, 1.96418236, 1.93645608,
1.94905155, 1.96164668])
for v1, v2 in izip(x1, self.x0):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in izip(x2, x2true):
self.assertAlmostEqual(v1, v2, 5)
def test_cpp_zero_ev(self):
print "\ntest zeroEV cpp"
x = self.x0.copy()
zev = self.topology._zeroEV_python(x)
czev = self.topology.cpp_topology.get_zero_modes(x)
self.assertEqual(len(czev), 6)
for ev, cev in izip(zev, czev):
for v1, v2 in izip(ev, cev):
self.assertAlmostEqual(v1, v2, 5)
def test_site_distance_squared(self):
print "\ntest site distance squared"
c0 = np.zeros(3)
c1 = np.ones(3)
p0 = self.p0.copy()
p1 = p0 + 1
site = self.system.make_otp()
d2 = site.distance_squared(c0, p0, c1, p1)
d2p = _sitedist(c1-c0, p0, p1, site.S, site.W, site.cog)
self.assertAlmostEqual(d2, 10.9548367929, 5)
def test_distance_squared(self):
print "\ntest distance squared"
x1 = self.x0.copy()
x2 = self.x0 + 1.1
d2 = self.topology.distance_squared(x1, x2)
d3 = self.topology._distance_squared_python(x1, x2)
self.assertAlmostEqual(d2, 38.9401810973, 5)
self.assertAlmostEqual(d2, d3, 5)
def test_distance_squared_grad(self):
print "\ntest distance squared grad"
x1 = self.x0.copy()
x2 = self.x0 + 1.1
grad = self.topology.distance_squared_grad(x1, x2)
g2 = self.topology._distance_squared_grad_python(x1, x2)
gtrue = np.array([-6.6 , -6.6 , -6.6 , -6.6 , -6.6 ,
-6.6 , -6.6 , -6.6 , -6.6 , -1.21579025,
-0.07013805, -1.2988823 , -1.21331786, -0.06984532, -1.28945301,
-1.2116105 , -0.06975828, -1.28362943])
for v1, v2 in izip(grad, gtrue):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in izip(grad, g2):
self.assertAlmostEqual(v1, v2, 5)
def test_measure_align(self):
print "\ntest measure align"
x1 = self.x0.copy()
x2 = self.x0 + 5.1
x2[-1] = x1[-1] + .1
x20 = x2.copy()
measure = MeasureRigidBodyCluster(self.topology)
measure.align(x1, x2)
def getdb(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
bh = system.get_basinhopping(db)
bh.run(20)
def getdb(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
bh = system.get_basinhopping(db)
bh.run(20)
def get_random_rbcoords(self):
otp = OTPCluster(self.nrigid)
ret = otp.get_random_minimized_configuration(tol=100.)
return ret.coords