def test_element_input_equivalence():
"""Test that the constructor for `Element` supports atomic numbers,
strings, and other `Element`s"""
expected = Element("H")
assert Element("H") == expected
assert Element("Hydrogen") == expected
assert Element("hydrogen") == expected # not case sensitive
assert Element(1) == expected
assert Element(expected) == expected
def test_input_equivalence(self):
""" Test that the constructor for `Element` supports atomic numbers,
strings, and other `Element`s """
expected = Element("H")
self.assertEqual(Element("H"), expected)
self.assertEqual(Element("Hydrogen"), expected)
self.assertEqual(Element("hydrogen"), expected) # not case sensitive
self.assertEqual(Element(1), expected)
self.assertEqual(Element(expected), expected)
def affe(atom, nG):
"""
Atomic form factors for electrons, for neutral atoms.
Parameters
----------
atom : skued.Atom, int, or str
Atomic number, atomic symbol, or Atom instance.
Atomic symbols are expected to be properly capitalized, e.g. ``As`` or ``W``.
nG : array_like
Scattering vector norm, in units of Angstroms:math:`^{-1}`. (:math:`|G| = 4 \pi s`).
Returns
-------
eff : `~numpy.ndarray`, dtype float
Atomic form factor for electron scattering.
Raises
------
ValueError : scattering information is not available, for example if the atomic number is larger than 103
"""
if isinstance(atom, (int, str)):
atom = Element(atom)
atomic_number = atom.atomic_number
try:
_, a1, b1, a2, b2, a3, b3, c1, d1, c2, d2, c3, d3 = scattering_params[
atomic_number
]
except KeyError:
raise ValueError(
"Scattering information for element Z={} is unavailable.".format(
atomic_number
)
)
# Parametrization of form factors is done in terms of q = 2 s = 2 pi |G|
q = nG / (2 * np.pi)
q2 = np.square(q)
sum1 = a1 / (q2 + b1) + a2 / (q2 + b2) + a3 / (q2 + b3)
sum2 = c1 * np.exp(-d1 * q2) + c2 * np.exp(-d2 * q2) + c3 * np.exp(-d3 * q2)
return sum1 + sum2
def aspherical_affe(atom, s):
"""
Aspherical atomic form factors for electron scattering.
Only atoms lighter than Xe (and including) are supported (Z <= 54).
Parameters
----------
atom : skued.Atom, int, or str
Atomic number, atomic symbol, or Atom instance.
Atomic symbols are expected to be properly capitalized, e.g. ``As`` or ``W``.
s : array_like
Scattering vector norm
Returns
-------
eff : `~numpy.ndarray`, dtype float
Atomic form factor for electron scattering.
Raises
------
ValueError : scattering information is not available, for example if the atomic number is larger than 54
References
----------
.. [#] Jin-Cheng Zheng, Lijun Wu and Yimei Zhu. "Aspherical electron scattering factors and their
parameterizations for elements from H to Xe" (2009). J. Appl. Cryst. vol 42, pp. 1043 - 1053.
"""
if isinstance(atom, (int, str)):
atom = Element(atom)
element = atom.element
params_a = aspherical_ff[element]["total"]["a"]
params_b = aspherical_ff[element]["total"]["b"]
s2 = np.square(np.asfarray(s))
result = np.zeros_like(s2)
for a, b in zip(params_a, params_b):
result += a * np.exp(-b * s2)
return result
nat = ntype(my_crystal)
print (" ntyp= ",nat,",",sep="")
print (" ecutwfc=80.0,")
print (" ecutrho=800.0,")
print (' xdm=.true.,')
print (" xdm_a1=0.6512,")
print (" xdm_a2=1.4633,\n/")
print ("&electrons")
print (" conv_thr = 1d-8\n/\n&ions\n/\n&cell\n/")
print ("ATOMIC_SPECIES")
for atm in my_crystal.chemical_composition:
ELE = str(atm)
ele = ELE.lower()
mass_number = Element(ele).mass
print (ele, " ",mass_number," ",ele,'.UPF',sep="")
print('\nATOMIC_POSITIONS crystal')
#print('\nATOMIC_POSITIONS angstrom')
################### loops for bottom layer ##################
#############################################################
bt0 = time.time()
bt1 = time.time()
tt1 = []
tt2 = []
def test_init_with_atomic_number(self):
""" Test that constructing an Element from a symbol or atomic number results in the same element """
for symbol in chemical_symbols:
from_symbol = Element(symbol)
from_number = Element(from_symbol.atomic_number)
self.assertEqual(from_number, from_symbol)
def test_invalid_element(self):
""" Test that an invalid chemical symbol will raise an error """
with self.assertRaises(ValueError):
Element("montreal")
def test_build(self):
""" Test that all valid chemical symbols can be used to create an Element instance """
for symbol in chemical_symbols:
Element(symbol)
def test_atomic_number_out_of_range(self):
""" Test that constructing an Element from an atomic number out-of-range raises a ValueError """
with self.assertRaises(ValueError):
Element(256)
def test_element_atomic_number_out_of_range():
"""Test that constructing an Element from an atomic number out-of-range raises a ValueError"""
with pytest.raises(ValueError):
Element(256)
def test_element_init_with_atomic_number(symbol):
"""Test that constructing an Element from a symbol or atomic number results in the same element"""
from_symbol = Element(symbol)
from_number = Element(from_symbol.atomic_number)
assert from_number == from_symbol
def test_element_invalid_element():
"""Test that an invalid chemical symbol will raise an error"""
with pytest.raises(ValueError):
Element("montreal")
def test_element_build(symbol):
"""Test that all valid chemical symbols can be used to create an Element instance"""
Element(symbol)