def test_axes_orthonorm(self):
import opan.utils.inertia as oui
from opan.utils.vector import orthonorm_check as onchk
axes = oui.principals(self.xyz.geoms[0], self.hess.atom_masses)[1]
on, nfail, ofail = onchk(axes, report=True)
self.assertTrue(on, msg="Norm failures: " + str(nfail) +
"; ortho failures: " + str(ofail))
def test_Utils_Vector_ONCheck_Trivial1D(self):
import numpy as np
from scipy import linalg as spla
from opan.utils.vector import orthonorm_check as onchk
vec = np.array(range(15))
vec = vec / spla.norm(vec)
c, nf, of = onchk(vec)
self.assertTrue(c)
self.assertIsNone(nf)
self.assertIsNone(of)
c, nf, of = onchk(vec, report=True)
self.assertTrue(c)
self.assertEqual(len(nf), 0)
self.assertEqual(len(of), 0)
def test_Utils_Vector_ONCheck_Trivial1D(self):
import numpy as np
from scipy import linalg as spla
from opan.utils.vector import orthonorm_check as onchk
vec = np.array(range(15))
vec = vec / spla.norm(vec)
c, nf, of = onchk(vec)
self.assertTrue(c)
self.assertIsNone(nf)
self.assertIsNone(of)
c, nf, of = onchk(vec, report=True)
self.assertTrue(c)
self.assertEqual(len(nf), 0)
self.assertEqual(len(of), 0)
def test_Utils_Vector_ONCheck_Trivial2D(self):
import numpy as np
from scipy import linalg as spla
from opan.utils.vector import orthonorm_check as onchk
from opan.utils.vector import ortho_basis as ob
vec = np.array([3.18, -2.25, 1.0005])
on1, on2 = ob(vec)
m = np.column_stack((vec / spla.norm(vec), on1, on2))
c, nf, of = onchk(m)
self.assertTrue(c)
self.assertIsNone(nf)
self.assertIsNone(of)
c, nf, of = onchk(m, report=True)
self.assertTrue(c)
self.assertEqual(len(nf), 0)
self.assertEqual(len(of), 0)
def test_Utils_Vector_ONCheck_Trivial2D(self):
import numpy as np
from scipy import linalg as spla
from opan.utils.vector import orthonorm_check as onchk
from opan.utils.vector import ortho_basis as ob
vec = np.array([3.18, -2.25, 1.0005])
on1, on2 = ob(vec)
m = np.column_stack((vec / spla.norm(vec), on1, on2))
c, nf, of = onchk(m)
self.assertTrue(c)
self.assertIsNone(nf)
self.assertIsNone(of)
c, nf, of = onchk(m, report=True)
self.assertTrue(c)
self.assertEqual(len(nf), 0)
self.assertEqual(len(of), 0)
def test_Utils_Vector_ONCheck_NonNormedVec(self):
import numpy as np
from opan.utils.vector import orthonorm_check as onchk
from opan.utils.vector import ortho_basis as ob
vec = np.array([-2.112, 2923.3, -0.2323])
on1, on2 = ob(vec)
m = np.column_stack((vec, on1, on2))
c, nf, of = onchk(m)
self.assertFalse(c)
self.assertIsNone(nf)
self.assertIsNone(of)
c, nf, of = onchk(m, report=True)
self.assertFalse(c)
self.assertEqual(len(of), 0)
self.assertEqual(len(nf), 1)
self.assertEqual(nf[0], 0)
def test_Utils_Vector_ONCheck_NonNormedVec(self):
import numpy as np
from opan.utils.vector import orthonorm_check as onchk
from opan.utils.vector import ortho_basis as ob
vec = np.array([-2.112, 2923.3, -0.2323])
on1, on2 = ob(vec)
m = np.column_stack((vec, on1, on2))
c, nf, of = onchk(m)
self.assertFalse(c)
self.assertIsNone(nf)
self.assertIsNone(of)
c, nf, of = onchk(m, report=True)
self.assertFalse(c)
self.assertEqual(len(of), 0)
self.assertEqual(len(nf), 1)
self.assertEqual(nf[0], 0)
def test_Utils_Vector_ONCheck_SkewedVec(self):
import numpy as np
from scipy import linalg as spla
from opan.utils.vector import orthonorm_check as onchk
from opan.utils.vector import ortho_basis as ob
vec = np.array([-6.277, 1.345, -23.8734])
offvec = np.subtract(vec, np.array([-3, 5, -12]))
offvec = offvec / spla.norm(offvec)
on1, on2 = ob(vec)
m = np.column_stack((offvec, on1, on2))
c, nf, of = onchk(m, report=True)
self.assertFalse(c)
self.assertEqual(len(nf), 0)
self.assertEqual(len(of), 2)
self.assertEqual(of[0], (0,1))
self.assertEqual(of[1], (0,2))
def test_Utils_Vector_ONCheck_SkewedVec(self):
import numpy as np
from scipy import linalg as spla
from opan.utils.vector import orthonorm_check as onchk
from opan.utils.vector import ortho_basis as ob
vec = np.array([-6.277, 1.345, -23.8734])
offvec = np.subtract(vec, np.array([-3, 5, -12]))
offvec = offvec / spla.norm(offvec)
on1, on2 = ob(vec)
m = np.column_stack((offvec, on1, on2))
c, nf, of = onchk(m, report=True)
self.assertFalse(c)
self.assertEqual(len(nf), 0)
self.assertEqual(len(of), 2)
self.assertEqual(of[0], (0, 1))
self.assertEqual(of[1], (0, 2))