def setUp(self):
self.natoms = 11
# self.x0 = _utils.random_configuration(3*11)
# self.x1 = _utils.random_configuration(3*11)
#
self.policy = TransformPolicyAtomicCluster()
self.measure = MeasureCartesian()
def setUp1(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.permlist = [range(self.natoms)]
self.measure = MeasureCartesian(permlist=self.permlist)
self.wrapped_optimize_permutations = lambda x1, x2: optimize_permutations(
x1, x2, self.permlist)
class TestFindRotation(unittest.TestCase):
def setUp(self):
self.natoms = 11
# self.x0 = _utils.random_configuration(3*11)
# self.x1 = _utils.random_configuration(3*11)
#
self.policy = TransformPolicyAtomicCluster()
self.measure = MeasureCartesian()
#
# self.rot = findrotation_kabsch(self.x0, self.x1, align_com=True)
def basic_test(self, x0, x1):
x0bk = x0.copy()
x1bk = x1.copy()
rot = findrotation_kabsch(x0, x1)
# rot = findrotation_kearsley(x0, x1)
self.assertTrue((x0 == x0bk).all())
self.assertTrue((x1 == x1bk).all())
self.policy.rotate(x1, rot)
self.assertLessEqual(self.measure.get_dist(x0, x1),
self.measure.get_dist(x0bk, x1bk))
def test1(self):
"""align two random configurations"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = _utils.random_configuration(3 * self.natoms)
# subtract center of mass
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
com = self.measure.get_com(x1)
self.policy.translate(x1, -com)
self.basic_test(x0, x1)
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)
class TestFindRotation(unittest.TestCase):
def setUp(self):
self.natoms = 11
# self.x0 = _utils.random_configuration(3*11)
# self.x1 = _utils.random_configuration(3*11)
#
self.policy = TransformPolicyAtomicCluster()
self.measure = MeasureCartesian()
#
# self.rot = findrotation_kabsch(self.x0, self.x1, align_com=True)
def basic_test(self, x0, x1):
x0bk = x0.copy()
x1bk = x1.copy()
rot = findrotation_kabsch(x0, x1)
# rot = findrotation_kearsley(x0, x1)
self.assertTrue((x0 == x0bk).all())
self.assertTrue((x1 == x1bk).all())
self.policy.rotate(x1, rot)
self.assertLessEqual(self.measure.get_dist(x0, x1), self.measure.get_dist(x0bk, x1bk))
def test1(self):
"""align two random configurations"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = _utils.random_configuration(3 * self.natoms)
# subtract center of mass
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
com = self.measure.get_com(x1)
self.policy.translate(x1, -com)
self.basic_test(x0, x1)
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 setUp(self):
self.natoms = 11
# self.x0 = _utils.random_configuration(3*11)
# self.x1 = _utils.random_configuration(3*11)
#
self.policy = TransformPolicyAtomicCluster()
self.measure = MeasureCartesian()
class TestOptimizePermutations(unittest.TestCase):
def setUp(self):
self.setUp1()
def setUp1(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.permlist = [range(self.natoms)]
self.measure = MeasureCartesian(permlist=self.permlist)
self.wrapped_optimize_permutations = lambda x1, x2: optimize_permutations(
x1, x2, self.permlist)
def basic_test(self, x0, x1):
x0bk = x0.copy()
x1bk = x1.copy()
perm = self.wrapped_optimize_permutations(x0, x1)
self.assertTrue((x0 == x0bk).all())
self.assertTrue((x1 == x1bk).all())
self.policy.permute(x1, perm)
self.assertLessEqual(self.measure.get_dist(x0, x1),
self.measure.get_dist(x0bk, x1bk))
def test1(self):
x0 = _utils.random_configuration(self.natoms * 3)
x1 = _utils.random_configuration(self.natoms * 3)
self.basic_test(x0, x1)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
self.policy.permute(
x1, _utils.random_permutation_permlist(self.permlist, self.natoms))
self.basic_test(x0, x1)
self.assertLess(np.abs(x0 - x1).max(), 1e-3)
class TestOptimizePermutations(unittest.TestCase):
def setUp(self):
self.setUp1()
def setUp1(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.permlist = [range(self.natoms)]
self.measure = MeasureCartesian(permlist=self.permlist)
self.wrapped_optimize_permutations = lambda x1, x2: optimize_permutations(x1, x2, self.permlist)
def basic_test(self, x0, x1):
x0bk = x0.copy()
x1bk = x1.copy()
perm = self.wrapped_optimize_permutations(x0, x1)
self.assertTrue((x0 == x0bk).all())
self.assertTrue((x1 == x1bk).all())
self.policy.permute(x1, perm)
self.assertLessEqual(self.measure.get_dist(x0, x1), self.measure.get_dist(x0bk, x1bk))
def test1(self):
x0 = _utils.random_configuration(self.natoms * 3)
x1 = _utils.random_configuration(self.natoms * 3)
self.basic_test(x0, x1)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
self.policy.permute(x1, _utils.random_permutation_permlist(self.permlist, self.natoms))
self.basic_test(x0, x1)
self.assertLess(np.abs(x0-x1).max(), 1e-3)
def setUp1(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.permlist = [range(self.natoms)]
self.measure = MeasureCartesian(permlist=self.permlist)
self.wrapped_optimize_permutations = lambda x1, x2: optimize_permutations(x1, x2, self.permlist)
