def test_reduce1():
atom = Atoms(['C', 'Au'])
atom = atom.sub(0)
atom1 = atom.reduce()
assert atom[0] == Atom[6]
assert len(atom) == 1
assert len(atom.atom) == 2
assert atom1[0] == Atom[6]
assert atom1[0] != Atom[8]
assert len(atom1) == 1
assert len(atom1.atom) == 1
atom.reduce(True)
assert atom[0] == Atom[6]
assert len(atom) == 1
assert len(atom.atom) == 1
def test_remove1():
atom = Atoms(['C', 'Au'])
atom = atom.remove(1)
atom = atom.reduce()
assert atom[0] == Atom[6]
assert len(atom) == 1
assert len(atom.atom) == 1
def test_reduce1(self):
atom = Atoms(['C', 'Au'])
atom = atom.sub(0)
atom = atom.reduce()
assert_true(atom[0] == Atom[6])
assert_true(len(atom) == 1)
assert_true(len(atom.atom) == 1)
def read_geometry(self, velocity=False, species_Z=False):
""" Returns a `Geometry` object from the XV file
Parameters
----------
species_Z : bool, optional
if ``True`` the atomic numbers are the species indices (useful when
reading the ChemicalSpeciesLabel block simultaneously).
velocity : bool, optional
also return the velocities in the file
Returns
-------
Geometry
velocity : only if `velocity` is true.
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
xyz = np.empty([na, 3], np.float64)
vel = np.empty([na, 3], np.float64)
atms = [None] * na
sp = np.empty([na], np.int32)
for ia in range(na):
line = list(map(float, self.readline().split()[:8]))
sp[ia] = int(line[0])
if species_Z:
atms[ia] = Atom(sp[ia])
else:
atms[ia] = Atom(int(line[1]))
xyz[ia, :] = line[2:5]
vel[ia, :] = line[5:8]
xyz *= Bohr2Ang
vel *= Bohr2Ang
# Ensure correct sorting
max_s = sp.max()
sp -= 1
# Ensure we can remove the atom after having aligned them
atms2 = Atoms(AtomUnknown(1000), na=na)
for i in range(max_s):
idx = (sp[:] == i).nonzero()[0]
if len(idx) == 0:
# Always ensure we have "something" for the unoccupied places
atms2[idx] = AtomUnknown(1000 + i)
else:
atms2[idx] = atms[idx[0]]
geom = Geometry(xyz, atms2.reduce(), sc=sc)
if velocity:
return geom, vel
return geom