def testTranslation(self):
coords = np.array([1., 2., 3., 4., 5., 6.])
# X
coords2 = coords.copy()
TransformCluster3D().translate(np.array([1., 0, 0])).apply(coords2)
self.assertLess(
np.linalg.norm(coords2 - np.array([2., 2., 3., 5., 5., 6.])),
1e-10)
# Y
coords2[:] = coords
TransformCluster3D().translate(np.array([0., 1, 0])).apply(coords2)
self.assertLess(
np.linalg.norm(coords2 - np.array([1., 3., 3., 4., 6., 6.])),
1e-10)
# Z
coords2[:] = coords
TransformCluster3D().translate(np.array([0., 0, 1])).apply(coords2)
self.assertLess(
np.linalg.norm(coords2 - np.array([1., 2., 4., 4., 5., 7.])),
1e-10)
# -x-y-z
coords2[:] = coords
TransformCluster3D().translate(np.array([-1., -2, -3])).apply(coords2)
self.assertLess(
np.linalg.norm(coords2 - np.array([0., 0., 0., 3., 3., 3.])),
1e-10)
def testReturnTypes(self):
trans = TransformCluster3D()
self.assertTrue(isinstance(trans.identity(), TransformCluster3D))
self.assertTrue(
isinstance(trans.translate(np.ones(3)), TransformCluster3D))
self.assertTrue(isinstance(trans.rotate(np.eye(3)),
TransformCluster3D))
def testRotate(self):
for i in xrange(100):
R = random_rotation()
transform = TransformCluster3D().rotate(R)
x = np.random.random(3 * 20)
x2 = x.reshape([-1, 3]).copy()
x2 = np.dot(R, x2.transpose()).transpose()
transform.apply(x)
self.assertLess(np.linalg.norm(x - x2.flatten()), 1e-10)
def testTransform(self):
# first combine 2 translations
coords = np.array([1., 2., 3., 4., 5., 6.])
coords2 = coords.copy()
transform = TransformCluster3D().translate(np.array([1., 2, 3]))
transform.transform(TransformCluster3D().translate(np.array([2., 3,
4])))
transform.apply(coords2)
self.assertLess(
np.linalg.norm(coords2 - np.array([4., 7., 10., 7., 10., 13.])),
1e-10)
for i in xrange(100):
dx1 = np.random.random(3)
R1 = random_rotation()
dx2 = np.random.random(3)
R2 = random_rotation()
transform = TransformCluster3D().translate(dx1)
transform.transform(TransformCluster3D().rotate(R1))
transform.transform(TransformCluster3D().translate(dx2))
transform.transform(TransformCluster3D().rotate(R2))
x = np.random.random(3 * 20)
x2 = x.reshape([-1, 3]).copy()
x2 = np.dot(R1, (x2 + dx1).transpose()).transpose()
x2 = np.dot(R2, (x2 + dx2).transpose()).transpose()
transform.apply(x)
self.assertLess(np.linalg.norm(x - x2.flatten()), 1e-10)
def testPermute(self):
for i in xrange(100):
coords2 = np.random.random(3 * 20)
coords = coords2.copy().reshape([-1, 3])
coords3 = coords2.copy()
transform = TransformCluster3D(nsites=20)
transform2 = TransformCluster3D(nsites=20)
perm = random_permutation(20)
transform.permute(perm)
coords = coords[perm]
transform2.transform(TransformCluster3D(nsites=20).permute(perm))
perm = random_permutation(20)
transform.permute(perm)
coords = coords[perm]
transform2.transform(TransformCluster3D(nsites=20).permute(perm))
transform.apply(coords2)
transform2.apply(coords3)
self.assertLess(np.linalg.norm(coords2 - coords.flatten()), 1e-10)
self.assertLess(np.linalg.norm(coords3 - coords.flatten()), 1e-10)
def apply_tests(self, f):
"""test that that a transofrmation object can reproduce the transformation in f"""
x = _utils.random_configuration(self.natoms * 3)
tform = TransformCluster3D(nsites=self.natoms)
xbkup = x.copy()
x2 = x.copy()
# do transormation
f(tform, x)
tform.apply(x2)
#x2 and x should be the same
self.assertLess(np.abs(x - x2).max(), 1e-3)
def testCombine(self):
for i in xrange(100):
dx1 = np.random.random(3)
R1 = random_rotation()
dx2 = np.random.random(3)
R2 = random_rotation()
transform = TransformCluster3D().translate(dx1)
transform.rotate(R1)
transform.translate(dx2)
transform.rotate(R2)
x = np.random.random(3 * 20)
x2 = x.reshape([-1, 3]).copy()
x2 = np.dot(R1, (x2 + dx1).transpose()).transpose()
x2 = np.dot(R2, (x2 + dx2).transpose()).transpose()
transform.apply(x)
self.assertLess(np.linalg.norm(x - x2.flatten()), 1e-10)
def testInitializationToIdentity(self):
coords = np.random.random(3 * 12)
coords2 = coords.copy()
TransformCluster3D().apply(coords2)
self.assertLess(np.linalg.norm(coords - coords2), 1e-10)
def setUp(self):
self.natoms = 11
self.tform = TransformCluster3D()
self.x = _utils.random_configuration(self.natoms * 3)
self.x2 = self.x.copy()