def zeroEV(self, x):
zev = []
ca = self.coords_adapter(x)
cv = self.coords_adapter(np.zeros(x.shape))
translate_rigid = zeroev.zeroEV_translation(ca.posRigid)
for v in translate_rigid:
cv.posRigid[:] = v
zev.append(cv.coords.copy())
#rotate_r = zeroev.zeroEV_rotation(ca.posRigid)
#rotate_aa =
transform = TransformAngleAxisCluster(self)
d = 1e-5
dx = x.copy()
transform.rotate(dx, rotations.aa2mx(np.array([d, 0, 0])))
self.align_path([x, dx])
dx -= x
dx /= np.linalg.norm(dx)
dy = x.copy()
transform.rotate(dy, rotations.aa2mx(np.array([0, d, 0])))
self.align_path([x, dy])
dy -= x
dy /= np.linalg.norm(dy)
dz = x.copy()
transform.rotate(dz, rotations.aa2mx(np.array([0, 0, d])))
self.align_path([x, dz])
dz -= x
dz /= np.linalg.norm(dz)
#print "Zero eigenvectors", zev
return zev + [dx, dy, dz]
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(list(range(1, 4)), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
def _zeroEV_python(self, x):
"""return a list of zero eigenvectors
This does both translational and rotational eigenvectors
"""
zev = []
ca = self.coords_adapter(x)
cv = self.coords_adapter(np.zeros(x.shape))
# get the zero eigenvectors corresponding to translation
translate_rigid = zeroev.zeroEV_translation(ca.posRigid)
for v in translate_rigid:
cv.posRigid[:] = v
zev.append(cv.coords.copy())
# get the zero eigenvectors corresponding to rotation
#rotate_r = zeroev.zeroEV_rotation(ca.posRigid)
#rotate_aa =
transform = TransformAngleAxisCluster(self)
d = 1e-5
dx = x.copy()
transform.rotate(dx, rotations.aa2mx(np.array([d, 0, 0])))
self.align_path([x, dx])
dx -= x
dx /= np.linalg.norm(dx)
dy = x.copy()
transform.rotate(dy, rotations.aa2mx(np.array([0, d, 0])))
self.align_path([x, dy])
dy -= x
dy /= np.linalg.norm(dy)
dz = x.copy()
transform.rotate(dz, rotations.aa2mx(np.array([0, 0, d])))
self.align_path([x, dz])
dz -= x
dz /= np.linalg.norm(dz)
#print "Zero eigenvectors", zev
return zev + [dx, dy, dz]
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(list(range(1,4)), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
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(list(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(list(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 zip(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 zip(x1, self.x0):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in zip(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 zip(zev, czev):
for v1, v2 in zip(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 = 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 zip(grad, gtrue):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in zip(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)
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(list(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(list(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 zip(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 zip(x1, self.x0):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in zip(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 zip(zev, czev):
for v1, v2 in zip(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 = 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 zip(grad, gtrue):
self.assertAlmostEqual(v1, v2, 5)
for v1, v2 in zip(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)
from pele.thermodynamics import normalmode_frequencies, logproduct_freq2
from tip4p_system import TIP4PSystem
from pele.angleaxis.aamindist import TransformAngleAxisCluster
from pele.utils import rotations
import numpy as np
from pele.mindist import PointGroupOrderCluster
from pele.angleaxis import ExactMatchAACluster
system = TIP4PSystem()
db = system.create_database(db="tip4p_8.sqlite")
pot = system.get_potential()
transform = TransformAngleAxisCluster(system.aasystem)
coords = db.minima()[0].coords
#coords = db.transition_states()[0].coords
energy = pot.getEnergy(coords)
#coords = np.loadtxt("2.txt").flatten()
print energy
match = ExactMatchAACluster(system.aasystem)
get_pgorder = PointGroupOrderCluster(match)
coords = db.minima()[0].coords
hess = pot.NumericalHessian(coords, eps=1e-4)
metric = system.aasystem.metric_tensor(coords)
print get_pgorder(coords)
frq = normalmode_frequencies(hess, metric)
print frq
fvib = logproduct_freq2(frq, 6)[1]
print fvib
