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 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 _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 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)
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)
