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 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 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 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 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 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 test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
x1 = x0.copy()
self.policy.rotate(x1, _utils.random_rotation())
self.basic_test(x0, x1)
self.assertLess(np.abs(x0 - x1).max(), 1e-3)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
x1 = x0.copy()
self.policy.rotate(x1, _utils.random_rotation())
self.basic_test(x0, x1)
self.assertLess(np.abs(x0-x1).max(), 1e-3)
def test_apply_rotation(self):
rot = _utils.random_rotation()
_utils.rotate(self.x2, rot)
self.tform.apply_rotation(self.x, rot)
self.assertLess(np.abs(self.x - self.x2).max(), 1e-3)
def test_apply_rotation(self):
rot = _utils.random_rotation()
_utils.rotate(self.x2, rot)
self.tform.apply_rotation(self.x, rot)
self.assertLess(np.abs(self.x - self.x2).max(), 1e-3)
