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 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 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)
class TestTransformation(unittest.TestCase):
def setUp(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.transform_list = [self.invert, self.rrot, self.rtrans, self.rperm]
def rrot(self, tform, coords):
"""apply random rotation to both coords and transformation object"""
mx = _utils.random_mx()
self.policy.rotate(coords, mx)
tform.rotate(mx)
def rtrans(self, tform, coords):
"""apply random translation to both coords and transformation object"""
xyz = _utils.random_translation()
self.policy.translate(coords, xyz)
tform.translate(xyz)
def invert(self, tform, coords):
"""apply inversion to both coords and transformation object"""
tform.invert()
self.policy.invert(coords)
def rperm(self, tform, coords):
"""apply random permutation to both coords and transformation object"""
perm = _utils.random_permutation(len(coords) / 3)
tform.permute(perm)
self.policy.permute(coords, perm)
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 fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(tform, x):
for f in reversed(flist):
# print f.__name__
f(tform, x)
return function_chain
def test_1(self):
"""run do_tests() on transformations
"""
for f in self.transform_list:
self.apply_tests(f)
def test_2(self):
"""run do_tests() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=2):
tform = self.fchain(flist)
self.apply_tests(tform)
def test_3(self):
"""run do_tests() on all combinations of length 3 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=3):
tform = self.fchain(flist)
self.apply_tests(tform)
def test_4(self):
"""run do_tests() on all combinations of length 3 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=4):
tform = self.fchain(flist)
self.apply_tests(tform)
def test_10(self):
"""run do_tests() on combinations of length 10 of the transformations
"""
maxiter = 2000
i = 0
for flist in itertools.product(self.transform_list, repeat=10):
tform = self.fchain(flist)
self.apply_tests(tform)
i += 1
if i > maxiter:
break
def setUp(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.transform_list = [self.invert, self.rrot, self.rtrans, self.rperm]
class TestTransformation(unittest.TestCase):
def setUp(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.transform_list = [self.invert, self.rrot, self.rtrans, self.rperm]
def rrot(self, tform, coords):
"""apply random rotation to both coords and transformation object"""
mx = _utils.random_mx()
self.policy.rotate(coords, mx)
tform.rotate(mx)
def rtrans(self, tform, coords):
"""apply random translation to both coords and transformation object"""
xyz = _utils.random_translation()
self.policy.translate(coords, xyz)
tform.translate(xyz)
def invert(self, tform, coords):
"""apply inversion to both coords and transformation object"""
tform.invert()
self.policy.invert(coords)
def rperm(self, tform, coords):
"""apply random permutation to both coords and transformation object"""
perm = _utils.random_permutation(len(coords) / 3)
tform.permute(perm)
self.policy.permute(coords, perm)
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 fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(tform, x):
for f in reversed(flist):
# print f.__name__
f(tform, x)
return function_chain
def test_1(self):
"""run do_tests() on transformations
"""
for f in self.transform_list:
self.apply_tests(f)
def test_2(self):
"""run do_tests() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=2):
tform = self.fchain(flist)
self.apply_tests(tform)
def test_3(self):
"""run do_tests() on all combinations of length 3 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=3):
tform = self.fchain(flist)
self.apply_tests(tform)
def test_4(self):
"""run do_tests() on all combinations of length 3 of the transformations
"""
for flist in itertools.product(self.transform_list, repeat=4):
tform = self.fchain(flist)
self.apply_tests(tform)
def test_10(self):
"""run do_tests() on combinations of length 10 of the transformations
"""
maxiter = 2000
i = 0
for flist in itertools.product(self.transform_list, repeat=10):
tform = self.fchain(flist)
self.apply_tests(tform)
i += 1
if i > maxiter:
break
def setUp(self):
self.natoms = 11
self.policy = TransformPolicyAtomicCluster()
self.transform_list = [self.invert, self.rrot, self.rtrans, self.rperm]