def _determine_inversion(self, permlist):
x = np.array(self.atom_positions).flatten()
xi = -x
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, xi):
if exact.check_match(x, xi, rot, invert):
self.inversion = exact._last_checked_rotation
return
def _determine_inversion(self, permlist):
x = np.array(self.atom_positions).flatten()
xi = -x
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, xi):
if exact.check_match(x, xi, rot, invert):
self.inversion = exact._last_checked_rotation
return
def _determine_rotational_symmetry(self, permlist):
x = np.array(self.atom_positions).flatten()
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, x):
if exact.check_match(x, x, rot, invert):
rot = exact._last_checked_rotation
exists = False
for rot2 in self.symmetries:
if np.linalg.norm(rot2 - rot) < 1e-6:
exists = True
break
if not exists:
self.symmetries.append(rot)
def _determine_rotational_symmetry(self, permlist):
x = np.array(self.atom_positions).flatten()
exact = ExactMatchAtomicCluster(permlist=permlist, can_invert=False)
for rot, invert in exact.standard_alignments(x, x):
if exact.check_match(x, x, rot, invert):
rot = exact._last_checked_rotation
exists=False
for rot2 in self.symmetries:
if np.linalg.norm(rot2 - rot) < 1e-6:
exists=True
break
if not exists:
self.symmetries.append(rot)
def testlj75(): # pragma: no cover
import numpy as np
coords = np.genfromtxt("tests/coords.lj75.gmin")
from pele.mindist import ExactMatchAtomicCluster
permlist = [list(range(75))]
match = ExactMatchAtomicCluster(permlist=permlist, can_invert=True)
calculator = PointGroupOrderCluster(match)
pgorder = calculator(coords)
print(pgorder)
def test1(self):
d = os.path.dirname(__file__)
fname = os.path.join(d, "coords.lj75.gmin.xyz")
xyz = read_xyz(open(fname, "r"))
coords = xyz.coords.reshape(-1)
print fname
self.assertEqual(coords.size, 75 * 3)
permlist = [range(75)]
match = ExactMatchAtomicCluster(permlist=permlist, can_invert=True)
calculator = PointGroupOrderCluster(match)
pgorder = calculator(coords)
# print pgorder
self.assertEqual(pgorder, 20)
def test1(self):
d = os.path.dirname(__file__)
dbfname = os.path.join(d, "lj75_very_small_pathsample.sqlite")
from pele.systems import LJCluster
natoms = 75
system = LJCluster(natoms)
db = system.create_database(dbfname, createdb=False)
permlist = [range(natoms)]
ts_min = list(db.minima()) + list(db.transition_states())
for m in ts_min:
match = ExactMatchAtomicCluster(permlist=permlist, can_invert=True)
calculator = PointGroupOrderCluster(match)
pgorder = calculator(m.coords)
self.assertEqual(pgorder, m.pgorder)
def test1(self):
from pele.systems import LJCluster
natoms = 13
system = LJCluster(natoms)
db = system.create_database()
bh = system.get_basinhopping(db)
bh.setPrinting(ostream=None)
while db.minima()[0].energy > -44.3:
bh.run(10)
m = db.minima()[0]
permlist = [range(natoms)]
match = ExactMatchAtomicCluster(permlist=permlist, can_invert=True)
calculator = PointGroupOrderCluster(match)
pgorder = calculator(m.coords)
# print pgorder
self.assertEqual(pgorder, 120)
def get_compare_exact(self, **kwargs):
"""this function quickly determines whether two clusters are identical
given translational, rotational and permutational symmeties
"""
permlist = self.get_permlist()
return ExactMatchAtomicCluster(permlist=permlist, **kwargs)
def get_compare_exact(self, **kwargs):
permlist = self.get_permlist()
return ExactMatchAtomicCluster(permlist=permlist, **kwargs)
class TestExactMatchAtomicCluster(unittest.TestCase):
def setUp(self):
self.natoms = 11
self.system = LJCluster(self.natoms)
self.match = ExactMatchAtomicCluster(
permlist=self.system.get_permlist(), can_invert=True)
def rc(self):
return self.system.get_random_configuration()
def rtrans(self, x):
vec3 = np.random.uniform(-1, 1, 3)
self.match.transform.translate(x, vec3)
def rrot(self, x):
aa = rotations.random_aa()
mx = rotations.aa2mx(aa)
self.match.transform.rotate(x, mx)
def invert(self, x):
self.match.transform.invert(x)
def rperm(self, x):
perm = range(self.natoms)
np.random.shuffle(perm)
self.match.transform.permute(x, perm)
def are_same_check(self, tform):
x1 = self.rc()
x2 = x1.copy()
tform(x1)
tform(x2)
x1_bkup = x1.copy()
x2_bkup = x2.copy()
self.assertTrue(self.match(x1, x2))
self.assertTrue((x1 == x1_bkup).all())
self.assertTrue((x2 == x2_bkup).all())
# transform = self.match.find_transformation(x1, x2)
# self.assertIsNotNone(transform, "the structures should compare exact")
# self.assertTrue((x1==x1_bkup).all())
# self.assertTrue((x2==x2_bkup).all())
# x2_tformed = x2.copy()
# self.match.apply_transformation(x2_tformed, transform)
# self.assertAlmostEqual(np.linalg.norm(x1_bkup - x2_tformed), 0., 3)
def find_transform_check(self, tform):
x1 = self.rc()
x2 = x1.copy()
tform(x1)
tform(x2)
x1_bkup = x1.copy()
x2_bkup = x2.copy()
transform = self.match.find_transformation(x1, x2)
# print "invert", transform.invert
# print "translate", transform.translation
# print "permute", transform.permutation
# print "rotate", transform.rotation
self.assertIsNotNone(transform, "the structures should compare exact")
self.assertTrue((x1 == x1_bkup).all(),
"the passed structures should not be modified")
self.assertTrue((x2 == x2_bkup).all(),
"the passed structures should not be modified")
# check that transform is the transformation that turns x2 into x1
x2_tformed = x2.copy()
self.match.apply_transformation(x2_tformed, transform)
self.assertAlmostEqual(np.linalg.norm(x1_bkup - x2_tformed), 0., 3)
def apply_checks(self, tform):
self.are_same_check(tform)
self.find_transform_check(tform)
def test_translate(self):
self.apply_checks(self.rtrans)
def test_rotate(self):
self.apply_checks(self.rrot)
def test_permute(self):
self.apply_checks(self.rperm)
def test_invert(self):
self.apply_checks(self.rperm)
def fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(x):
for f in reversed(flist):
f(x)
return function_chain
def test_2(self):
# run apply_checks() on all combinations of length 2 of the transformations
flist_all = [self.invert, self.rrot, self.rtrans, self.rperm]
for flist in itertools.product(flist_all, repeat=2):
tform = self.fchain(flist)
self.apply_checks(tform)
def test_3(self):
# run apply_checks() on all combinations of lenth 3 of the transformations
flist_all = [self.invert, self.rrot, self.rtrans, self.rperm]
for flist in itertools.product(flist_all, repeat=3):
tform = self.fchain(flist)
self.apply_checks(tform)
def test_4(self):
# run apply_checks() on all combinations of lenth 4 of the transformations
flist_all = [self.invert, self.rrot, self.rtrans, self.rperm]
for flist in itertools.product(flist_all, repeat=4):
tform = self.fchain(flist)
self.apply_checks(tform)
def setUp(self):
self.natoms = 11
self.system = LJCluster(self.natoms)
self.match = ExactMatchAtomicCluster(
permlist=self.system.get_permlist(), can_invert=True)
def get_compare_exact(self, **kwargs):
permlist = [range(self.natoms)]
return ExactMatchAtomicCluster(permlist=permlist, **kwargs)
def setUp(self):
self.natoms = 11
self.system = LJCluster(self.natoms)
self.match = ExactMatchAtomicCluster(permlist=self.system.get_permlist(), can_invert=True)
class TestExactMatchAtomicCluster(unittest.TestCase):
def setUp(self):
self.natoms = 11
self.system = LJCluster(self.natoms)
self.match = ExactMatchAtomicCluster(permlist=self.system.get_permlist(), can_invert=True)
def rc(self):
return self.system.get_random_configuration()
def rtrans(self, x):
vec3 = np.random.uniform(-1,1,3)
self.match.transform.translate(x, vec3)
def rrot(self, x):
aa = rotations.random_aa()
mx = rotations.aa2mx(aa)
self.match.transform.rotate(x, mx)
def invert(self, x):
self.match.transform.invert(x)
def rperm(self, x):
perm = range(self.natoms)
np.random.shuffle(perm)
self.match.transform.permute(x, perm)
def are_same_check(self, tform):
x1 = self.rc()
x2 = x1.copy()
tform(x1)
tform(x2)
x1_bkup = x1.copy()
x2_bkup = x2.copy()
self.assertTrue(self.match(x1, x2))
self.assertTrue((x1==x1_bkup).all())
self.assertTrue((x2==x2_bkup).all())
# transform = self.match.find_transformation(x1, x2)
# self.assertIsNotNone(transform, "the structures should compare exact")
# self.assertTrue((x1==x1_bkup).all())
# self.assertTrue((x2==x2_bkup).all())
# x2_tformed = x2.copy()
# self.match.apply_transformation(x2_tformed, transform)
# self.assertAlmostEqual(np.linalg.norm(x1_bkup - x2_tformed), 0., 3)
def find_transform_check(self, tform):
x1 = self.rc()
x2 = x1.copy()
tform(x1)
tform(x2)
x1_bkup = x1.copy()
x2_bkup = x2.copy()
transform = self.match.find_transformation(x1, x2)
# print "invert", transform.invert
# print "translate", transform.translation
# print "permute", transform.permutation
# print "rotate", transform.rotation
self.assertIsNotNone(transform, "the structures should compare exact")
self.assertTrue((x1==x1_bkup).all(), "the passed structures should not be modified")
self.assertTrue((x2==x2_bkup).all(), "the passed structures should not be modified")
# check that transform is the transformation that turns x2 into x1
x2_tformed = x2.copy()
self.match.apply_transformation(x2_tformed, transform)
self.assertAlmostEqual(np.linalg.norm(x1_bkup - x2_tformed), 0., 3)
def apply_checks(self, tform):
self.are_same_check(tform)
self.find_transform_check(tform)
def test_translate(self):
self.apply_checks(self.rtrans)
def test_rotate(self):
self.apply_checks(self.rrot)
def test_permute(self):
self.apply_checks(self.rperm)
def test_invert(self):
self.apply_checks(self.rperm)
def fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(x):
for f in reversed(flist):
f(x)
return function_chain
def test_2(self):
# run apply_checks() on all combinations of length 2 of the transformations
flist_all = [self.invert, self.rrot, self.rtrans, self.rperm]
for flist in itertools.product(flist_all, repeat=2):
tform = self.fchain(flist)
self.apply_checks(tform)
def test_3(self):
# run apply_checks() on all combinations of lenth 3 of the transformations
flist_all = [self.invert, self.rrot, self.rtrans, self.rperm]
for flist in itertools.product(flist_all, repeat=3):
tform = self.fchain(flist)
self.apply_checks(tform)
def test_4(self):
# run apply_checks() on all combinations of lenth 4 of the transformations
flist_all = [self.invert, self.rrot, self.rtrans, self.rperm]
for flist in itertools.product(flist_all, repeat=4):
tform = self.fchain(flist)
self.apply_checks(tform)