def test_toatomicorbital_q0(self):
rf = r_f(6)
orb = SphericalOrbital(0, rf, 2.)
ao = orb.toAtomicOrbital()
assert len(ao) == 1
assert ao[0].q0 == 2.
# Check m and l
for l in range(1, 5):
orb = SphericalOrbital(l, rf, 2.)
ao = orb.toAtomicOrbital()
assert ao[0].q0 == pytest.approx(2. / (2 * l + 1))
def read_basis(self):
""" Returns data associated with the ion.xml file """
# Get the element-tree
ET = ElementTree(None, self.file)
root = ET.getroot()
# Get number of orbitals
label = root.find('label').text.strip()
Z = int(root.find('z').text) # atomic number
mass = float(root.find('mass').text)
# Read in the PAO's
paos = root.find('paos')
# Now loop over all orbitals
orbital = []
# All orbital data
Bohr2Ang = unit_convert('Bohr', 'Ang')
for orb in paos:
n = int(orb.get('n'))
l = int(orb.get('l'))
z = int(orb.get('z')) # zeta
q0 = float(orb.get('population'))
P = not int(orb.get('ispol')) == 0
# Radial components
rad = orb.find('radfunc')
npts = int(rad.find('npts').text)
# Grid spacing in Bohr (conversion is done later
# because the normalization is easier)
delta = float(rad.find('delta').text)
# Read in data to a list
dat = list(map(float, rad.find('data').text.split()))
# Since the readed data has fewer significant digits we
# might as well re-create the table of the radial component.
r = aranged(npts) * delta
# To get it per Ang**3
# TODO, check that this is correct.
# The fact that we have to have it normalized means that we need
# to convert psi /sqrt(Bohr**3) -> /sqrt(Ang**3)
# \int psi^\dagger psi == 1
psi = arrayd(dat[1::2]) * r**l / Bohr2Ang**(3. / 2.)
# Create the sphericalorbital and then the atomicorbital
sorb = SphericalOrbital(l, (r * Bohr2Ang, psi), q0)
# This will be -l:l (this is the way siesta does it)
orbital.extend(sorb.toAtomicOrbital(n=n, Z=z, P=P))
# Now create the atom and return
return Atom(Z, orbital, mass=mass, tag=label)
def read_basis(self):
""" Returns data associated with the ion.xml file """
no = len(self._dimension('norbs'))
# Get number of orbitals
label = self.Label.strip()
Z = int(self.Atomic_number)
mass = float(self.Mass)
# Retrieve values
orb_l = self._variable('orbnl_l')[:] # angular quantum number
orb_n = self._variable('orbnl_n')[:] # principal quantum number
orb_z = self._variable('orbnl_z')[:] # zeta
orb_P = self._variable(
'orbnl_ispol')[:] > 0 # polarization shell, or not
orb_q0 = self._variable('orbnl_pop')[:] # q0 for the orbitals
orb_delta = self._variable('delta')[:] # delta for the functions
orb_psi = self._variable('orb')[:, :]
# Now loop over all orbitals
orbital = []
# All orbital data
Bohr2Ang = unit_convert('Bohr', 'Ang')
for io in range(no):
n = orb_n[io]
l = orb_l[io]
z = orb_z[io]
P = orb_P[io]
# Grid spacing in Bohr (conversion is done later
# because the normalization is easier)
delta = orb_delta[io]
# Since the readed data has fewer significant digits we
# might as well re-create the table of the radial component.
r = aranged(orb_psi.shape[1]) * delta
# To get it per Ang**3
# TODO, check that this is correct.
# The fact that we have to have it normalized means that we need
# to convert psi /sqrt(Bohr**3) -> /sqrt(Ang**3)
# \int psi^\dagger psi == 1
psi = orb_psi[io, :] * r**l / Bohr2Ang**(3. / 2.)
# Create the sphericalorbital and then the atomicorbital
sorb = SphericalOrbital(l, (r * Bohr2Ang, psi), orb_q0[io])
# This will be -l:l (this is the way siesta does it)
orbital.extend(sorb.toAtomicOrbital(n=n, Z=z, P=P))
# Now create the atom and return
return Atom(Z, orbital, mass=mass, tag=label)
def test_toatomicorbital1(self):
rf = r_f(6)
orb = SphericalOrbital(0, rf)
ao = orb.toAtomicOrbital()
assert len(ao) == 1
assert ao[0].l == orb.l
assert ao[0].m == 0
# Check m and l
for l in range(1, 5):
orb = SphericalOrbital(l, rf)
ao = orb.toAtomicOrbital()
assert len(ao) == 2 * l + 1
m = -l
for a in ao:
assert a.l == orb.l
assert a.m == m
m += 1
orb = SphericalOrbital(1, rf)
ao = orb.toAtomicOrbital(1)
assert ao.l == orb.l
assert ao.m == 1
ao = orb.toAtomicOrbital(-1)
assert ao.l == orb.l
assert ao.m == -1
ao = orb.toAtomicOrbital(0)
assert ao.l == orb.l
assert ao.m == 0
ao = orb.toAtomicOrbital([0, -1, 1])
for a in ao:
assert a.l == orb.l
assert ao[0].m == 0
assert ao[1].m == -1
assert ao[2].m == 1
def test_toatomicorbital2(self):
rf = r_f(6)
orb = SphericalOrbital(1, rf)
with pytest.raises(ValueError):
ao = orb.toAtomicOrbital(2)
def test_toatomicorbital2(self):
rf = r_f(6)
orb = SphericalOrbital(1, rf)
ao = orb.toAtomicOrbital(2)