def check_electronegativity_2(formula):
pauling_count = 0
comp = mg.Composition(formula)
reduce_formula = comp.get_el_amt_dict()
list_of_elements = list(reduce_formula.keys())
max_num = max(reduce_formula.values())
for i, ele_a in enumerate(list_of_elements):
paul_a = smact.Element(ele_a).pauling_eneg
for ox_a in smact.Element(ele_a).oxidation_states:
for j, ele_b in enumerate(list_of_elements[i + 1:]):
paul_b = smact.Element(ele_b).pauling_eneg
for ox_b in smact.Element(ele_b).oxidation_states:
# Puts elements, oxidation states and electronegativites into lists for convenience #
elements = [ele_a, ele_b]
oxidation_states = [ox_a, ox_b]
pauling_electro = [paul_a, paul_b]
# Checks if the electronegativity makes sense and if the combination is charge neutral #
electroneg_makes_sense = pauling_test(
oxidation_states, pauling_electro, elements)
cn_e, cn_r = neutral_ratios([ox_a, ox_b],
threshold=int(max_num))
if cn_e:
if electroneg_makes_sense:
pauling_count = pauling_count + 1
for num in cn_r:
if tuple(reduce_formula.values()) == num:
# print('{0:2s}{1:3d} {2:2s}{3:3d} {4:2s}{5:3d}'.format(ele_a, ox_a, ele_b,
# ox_b, ele_c, ox_c))
return True
print('Number of combinations = {0}'.format(pauling_count))
print("--- {0} seconds to run ---".format(time.time() - start_time))
return False
def check_neutrality_2(formula):
charge_neutral_count = 0
comp = mg.Composition(formula)
reduce_formula = comp.get_el_amt_dict()
list_of_elements = list(reduce_formula.keys())
# stoichs = np.array(list(reduce_formula.values())).astype(np.int32)[:,np.newaxis]
max_num = max(reduce_formula.values())
for i, ele_a in enumerate(list_of_elements):
for ox_a in smact.Element(ele_a).oxidation_states:
for j, ele_b in enumerate(list_of_elements[i+1:]):
for ox_b in smact.Element(ele_b).oxidation_states:
# Checks if the combination is charge neutral before printing it out! #
# neutral_ratios(oxidations, stoichs=False, threshold=5) #speed up by providing stoichs
# cn_e, cn_r = neutral_ratios([ox_a, ox_b], threshold = int(max_num))
cn_e, cn_r = neutral_ratios([ox_a, ox_b], threshold = int(max_num))
if cn_e:
for num in cn_r:
if tuple(reduce_formula.values()) == num:
return True
# print(cn_e)
# print(cn_r)
# print(ox_a, ox_b, ox_c)
# charge_neutral_count = charge_neutral_count + 1
# print('{0:3s} {1:3s} {2:3s}'.format(ele_a, ele_b, ele_c))
print('Number of combinations = {0}'.format(charge_neutral_count))
print("--- {0} seconds to run ---".format(time.time() - start_time))
return False
def check_neutrality_4(formula):
charge_neutral_count = 0
comp = mg.Composition(formula)
reduce_formula = comp.get_el_amt_dict()
list_of_elements = list(reduce_formula.keys())
max_num = max(reduce_formula.values())
for i, ele_a in enumerate(list_of_elements):
for ox_a in smact.Element(ele_a).oxidation_states:
for j, ele_b in enumerate(list_of_elements[i+1:]):
for ox_b in smact.Element(ele_b).oxidation_states:
for k, ele_c in enumerate(list_of_elements[i+j+2:]):
for ox_c in smact.Element(ele_c).oxidation_states:
for m, ele_d in enumerate(list_of_elements[i+j+k+3:]):
for ox_d in smact.Element(ele_d).oxidation_states:
# Checks if the combination is charge neutral before printing it out! #
cn_e, cn_r = neutral_ratios([ox_a, ox_b, ox_c, ox_d], threshold = int(max_num))
if cn_e:
for num in cn_r:
if tuple(reduce_formula.values()) == num:
return True
# print(cn_e)
# print(cn_r)
# print(ox_a, ox_b, ox_c)
# charge_neutral_count = charge_neutral_count + 1
# print('{0:3s} {1:3s} {2:3s}'.format(ele_a, ele_b, ele_c))
print('Number of combinations = {0}'.format(charge_neutral_count))
print("--- {0} seconds to run ---".format(time.time() - start_time))
return False
def test_smact_test(self):
Na, Fe, Cl = (smact.Element(label) for label in ('Na', 'Fe', 'Cl'))
self.assertEqual(smact.screening.smact_test([Na, Fe, Cl], threshold=2),
[(('Na', 'Fe', 'Cl'), (1, -1, -1), (2, 1, 1)),
(('Na', 'Fe', 'Cl'), (1, 1, -1), (1, 1, 2))])
self.assertEqual(
len(smact.screening.smact_test([Na, Fe, Cl], threshold=8)), 77)
def test_pauling_test(self):
Sn, S = (smact.Element(label) for label in ('Sn', 'S'))
self.assertTrue(
smact.screening.pauling_test(
(+2, -2),
(Sn.pauling_eneg, S.pauling_eneg),
))
self.assertFalse(
smact.screening.pauling_test((-2, +2),
(Sn.pauling_eneg, S.pauling_eneg)))
self.assertFalse(
smact.screening.pauling_test(
(-2, -2, +2),
(S.pauling_eneg, S.pauling_eneg, Sn.pauling_eneg),
symbols=('S', 'S', 'Sn'),
repeat_anions=False))
self.assertTrue(
smact.screening.pauling_test(
(-2, -2, +2),
(S.pauling_eneg, S.pauling_eneg, Sn.pauling_eneg),
symbols=('S', 'S', 'Sn'),
repeat_cations=False))
self.assertFalse(
smact.screening.pauling_test(
(-2, +2, +2),
(S.pauling_eneg, Sn.pauling_eneg, Sn.pauling_eneg),
symbols=('S', 'Sn', 'Sn'),
repeat_cations=False))
self.assertTrue(
smact.screening.pauling_test(
(-2, +2, +2),
(S.pauling_eneg, Sn.pauling_eneg, Sn.pauling_eneg),
symbols=('S', 'Sn', 'Sn'),
repeat_anions=False))
def check_electronegativity_4(formula):
pauling_count = 0
comp = mg.Composition(formula)
reduce_formula = comp.get_el_amt_dict()
list_of_elements = list(reduce_formula.keys())
stoichs = list(
np.array(list(reduce_formula.values())).astype(np.int32)[:,
np.newaxis])
max_num = max(reduce_formula.values())
for i, ele_a in enumerate(list_of_elements):
paul_a = smact.Element(ele_a).pauling_eneg
for ox_a in smact.Element(ele_a).oxidation_states:
for j, ele_b in enumerate(list_of_elements[i + 1:]):
paul_b = smact.Element(ele_b).pauling_eneg
for ox_b in smact.Element(ele_b).oxidation_states:
for k, ele_c in enumerate(list_of_elements[i + j + 2:]):
paul_c = smact.Element(ele_c).pauling_eneg
for ox_c in smact.Element(ele_c).oxidation_states:
for m, ele_d in enumerate(
list_of_elements[i + j + k + 3:]):
paul_d = smact.Element(ele_d).pauling_eneg
for ox_d in smact.Element(
ele_d).oxidation_states:
# Puts elements, oxidation states and electronegativites into lists for convenience #
elements = [ele_a, ele_b, ele_c, ele_d]
oxidation_states = [ox_a, ox_b, ox_c, ox_d]
pauling_electro = [
paul_a, paul_b, paul_c, paul_d
]
if None in pauling_electro:
print(
"No pauling electronegativity data"
)
return False
# Checks if the electronegativity makes sense and if the combination is charge neutral #
electroneg_makes_sense = pauling_test(
oxidation_states, pauling_electro,
elements)
cn_e, cn_r = neutral_ratios(
[ox_a, ox_b, ox_c, ox_d],
stoichs=stoichs,
threshold=int(max_num))
if cn_e:
if electroneg_makes_sense:
pauling_count = pauling_count + 1
for num in cn_r:
if tuple(reduce_formula.values(
)) == num:
# print('{0:2s}{1:3d} {2:2s}{3:3d} {4:2s}{5:3d}'.format(ele_a, ox_a, ele_b,
# ox_b, ele_c, ox_c))
return True
# print('Number of combinations = {0}'.format(pauling_count))
# print("--- {0} seconds to run ---".format(time.time() - start_time))
return False
def test_eneg_states_test_alternate(self):
Na, Fe, Cl = (smact.Element(label) for label in ('Na', 'Fe', 'Cl'))
self.assertTrue(
smact.screening.eneg_states_test_alternate(
[1, 3, -1],
[Na.pauling_eneg, Fe.pauling_eneg, Cl.pauling_eneg]))
self.assertFalse(
smact.screening.eneg_states_test_alternate(
[-1, 3, 1],
[Na.pauling_eneg, Fe.pauling_eneg, Cl.pauling_eneg]))
def check_neutrality_8(formula):
charge_neutral_count = 0
comp = mg.Composition(formula)
reduce_formula = comp.get_el_amt_dict()
list_of_elements = list(reduce_formula.keys())
stoichs = list(
np.array(list(reduce_formula.values())).astype(np.int32)[:,np.newaxis]
)
max_num = max(reduce_formula.values())
for element in reduce_formula.keys():
print(len(smact.Element(element).oxidation_states), end = ",")
for i, ele_a in enumerate(list_of_elements):
for ox_a in smact.Element(ele_a).oxidation_states:
for j, ele_b in enumerate(list_of_elements[i+1:]):
for ox_b in smact.Element(ele_b).oxidation_states:
for k, ele_c in enumerate(list_of_elements[i+j+2:]):
for ox_c in smact.Element(ele_c).oxidation_states:
for m, ele_d in enumerate(list_of_elements[i+j+k+3:]):
for ox_d in smact.Element(ele_d).oxidation_states:
for n, ele_e in enumerate(list_of_elements[i+j+k+m+4:]):
for ox_e in smact.Element(ele_e).oxidation_states:
for p, ele_f in enumerate(list_of_elements[i+j+k+m+n+5:]):
for ox_f in smact.Element(ele_f).oxidation_states:
for q, ele_g in enumerate(list_of_elements[i+j+k+m+n+p+6:]):
for ox_g in smact.Element(ele_g).oxidation_states:
for s, ele_h in enumerate(list_of_elements[i+j+k+m+n+p+q+7:]):
for ox_h in smact.Element(ele_h).oxidation_states:
# Checks if the combination is charge neutral before printing it out! #
cn_e, cn_r = neutral_ratios([ox_a, ox_b, ox_c, ox_d, ox_e, ox_f, ox_g, ox_h], stoichs = stoichs, threshold = int(max_num))
if cn_e:
for num in cn_r:
if tuple(reduce_formula.values()) == num:
return True
# print(cn_e)
# print(cn_r)
# print(ox_a, ox_b, ox_c)
# charge_neutral_count = charge_neutral_count + 1
# print('{0:3s} {1:3s} {2:3s}'.format(ele_a, ele_b, ele_c))
print('Number of combinations = {0}'.format(charge_neutral_count))
print("--- {0} seconds to run ---".format(time.time() - start_time))
return False
def test_ml_rep_generator(self):
Pb, O = (smact.Element(label) for label in ('Pb', 'O'))
PbO2_ml = [
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.6666666666666666, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.3333333333333333, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0
]
self.assertEqual(smact.screening.ml_rep_generator(['Pb', 'O'], [1, 2]),
PbO2_ml)
self.assertEqual(smact.screening.ml_rep_generator([Pb, O], [1, 2]),
PbO2_ml)
def eneg_mulliken(element):
"""Get Mulliken electronegativity from the IE and EA.
Arguments:
symbol (smact.Element or str): Element object or symbol
Returns:
mulliken (float): Mulliken electronegativity
"""
if type(element) == str:
element = smact.Element(element)
elif type(element) != smact.Element:
raise Exception("Unexpected type: {0}".format(type(element)))
mulliken = (element.ionpot + element.e_affinity) / 2.0
return mulliken
def possible_elements(elements, oxidations):
"""Identify possible atoms to occupy a site
Args:
elements:
oxidations:
Returns:
Array of atoms
"""
atoms = []
for element in elements:
elemental_oxidations = smact.Element(element).oxidation_states
for ox_state_a in oxidations:
for element_ox in elemental_oxidations:
if int(element_ox) == int(ox_state_a):
atoms.append(element)
return atoms
def main():
crystal_elements = input(
'Which elements? Separate chemical symbols with a space. ')
crystal_elements = crystal_elements.split()
a_lattices = [lp.fcc, lp.bcc, lp.hcp, lp.diamond, lp.bct]
b_lattices = [lp.rocksalt, lp.b2, lp.zincblende, lp.wurtzite, lp.b10]
e_lattices = [lp.cubic_perovskite]
# Processing Lattices
#------------------------------------------------------------------------------------------
## A-types
print(" \n=========================================")
print(" AAA ####### ## ## ##### #####")
print(" AA A ## ## ## ## ## ##")
print(" AAAAAA #### ## ## ##### #####")
print(" AA AA ## ## ## ##")
print("AA AA ## ## ## #####")
print("=========================================")
print(" \n ### A type lattices ###\n ")
for lattice in a_lattices:
print((' \n===============\n ') + lattice.__name__.upper() +
(' Lattice \n===============\n '))
for elements in crystal_elements:
x = smact.Element(elements)
a, b, c, alpha, beta, gamma = lattice(x.covalent_radius)
print(elements, "%.2f" % a, "%.2f" % b, "%.2f" % c, "%.1f" % alpha,
"%.1f" % beta, "%.1f" % gamma)
print(
' \n Key :: Element a b c alpha beta gamma \n///////////////////////////////////////////////////////////////////////////////////////\n '
)
oxidation = []
coordination = []
i = 0
for elements in crystal_elements:
poss_ox = []
poss_cood = []
with open('data/shannon_radii.csv', 'rU') as f:
reader = csv.reader(f)
for row in reader:
if row[0] == elements:
poss_ox.append(row[1])
poss_cood.append(row[2])
poss_ox_clean = [] ### Duplicates removed
for ox in poss_ox:
if ox not in poss_ox_clean:
poss_ox_clean.append(ox)
print(elements)
print(poss_ox_clean)
if len(poss_ox_clean) == 1:
oxidation.append(int(poss_ox_clean[0]))
else:
oxidation.append(int(input('Oxidation state of ' + elements +
' ')))
poss_co_clean = [] ### Duplicates removed
with open('data/shannon_radii.csv', 'rU') as f:
reader = csv.reader(f)
poss_cood = []
for row in reader:
if row[0] == elements and int(row[1]) == int(oxidation[-1]):
poss_cood.append(row[2])
for co in poss_cood:
if co not in poss_co_clean:
poss_co_clean.append(co)
print(elements)
print(poss_co_clean)
if len(poss_co_clean) == 1:
coordination.append(poss_co_clean[0])
else:
coordination.append(
input('Coordination state of ' + elements + ' '))
print(elements, oxidation[i], coordination[i])
i += 1
## B-types
#-------------------------------------------------------------------------------------#
print(" \n=========================================")
print(" BBBB ####### ## ## ##### #####")
print(" BB BB ## ## ## ## ## ##")
print(" BBBB ### ## ## ##### #####")
print(" BB BB ## ## ## ##")
print("BBBB ## ## ## #####")
print("=========================================")
print(" \n ### B type lattices ###\n ")
for lattice in b_lattices:
print((' \n===============\n ') + lattice.__name__.upper() +
(' Lattice \n===============\n '))
shannon_radius = []
for i, elements in enumerate(crystal_elements):
print(elements, oxidation[i], coordination[i])
x = smact.Species(elements, oxidation[i], coordination[i])
shannon_radius.append(float(x.shannon_radius))
a, b, c, alpha, beta, gamma = lattice(shannon_radius)
if lattice.__name__ == 'wurtzite':
inner_space = a * (6**0.5) - (4 * shannon_radius[0])
print("With a gap in the middle of " + "%.2f" % inner_space +
" (diameter)")
print(crystal_elements[0:2], "%.2f" % a, "%.2f" % b, "%.2f" % c,
"%.1f" % alpha, "%.1f" % beta, "%.1f" % gamma)
# E Types
#-------------------------------------------------------------------------------------#
print(" \n=========================================")
print(" EEEEE ####### ## ## ##### #####")
print(" EE ## ## ## ## ## ##")
print(" EEEE ### ## ## ##### #####")
print(" EE ## ## ## ##")
print("EEEEE ## ## ## #####")
print("=========================================")
print(" \n ### E type lattices ###\n ")
for lattice in e_lattices:
print((' \n===============\n ') + lattice.__name__.upper() +
(' Lattice \n===============\n '))
shannon_radius = []
for i, elements in enumerate(crystal_elements):
print(elements, oxidation[i], coordination[i])
x = smact.Species(elements, oxidation[i], coordination[i])
shannon_radius.append(float(x.shannon_radius))
a, b, c, space, alpha, beta, gamma = lattice(shannon_radius)
print(crystal_elements[0:], "%.2f" % a, "%.2f" % b, "%.2f" % c,
"%.1f" % alpha, "%.1f" % beta, "%.1f" % gamma)
print("With a gap in the middle of " + "%.2f" % space + " (diameter)")
#!/usr/bin/env python
import smact
from numpy import product,sqrt
from smact.data import get_covalent
from scipy.constants import hbar, m_e
# Get element info
An =raw_input("Enter Anion Symbol: ")
Cat =raw_input("Enter Cation Symbol: ")
eig_an = smact.Element(An).eig
eig_cat = smact.Element(Cat).eig
# Calculations
V2 = (2.16*(hbar)**2)/m_e*(((get_covalent(An)**-9))+((get_covalent(Cat))**-9)**2)
V3 = (eig_cat - eig_an)/2
Ev = ((eig_cat + eig_an)/2) - (sqrt((V2**2)+(V3**2)))
print An, get_covalent(An)
print Cat, get_covalent(Cat)
print "V2:", V2, "V3:", V3
print "Valence Band Maximum = ", Ev
row[1]) in site_B.oxidation_states:
B_list.append([row[0], float(row[1]), float(row[4])])
# ## Iterative search
# Having constructed potential element lists for each of the sites we now do an iterative search through all poaaible combinations, applying different levels of screening.
# 1. A =/= B.
# 2. Charge neutrality.
# 3. Goldschmidt tolerance factors.
# 4. Environmental screening (greater HHI resource than CZTS).
# In[7]:
elements_dict = {}
for symbol, _, __ in A_list + B_list + C_list:
if symbol not in elements_dict:
elements_dict.update({symbol: smact.Element(symbol)})
# In[11]:
charge_balanced = []
goldschmidt_cubic = []
goldschmidt_ortho = []
a_too_large = []
A_B_similar = []
pauling_perov = []
anion_stats = []
hhi_cdte = 2904
enviro_perovskites = 0
total = 0
for C_sym, C_ox, C_r in C_list:
C_el = elements_dict[C_sym]
def check_electronegativity_8(formula):
pauling_count = 0
comp = mg.Composition(formula)
reduce_formula = comp.get_el_amt_dict()
list_of_elements = list(reduce_formula.keys())
max_num = max(reduce_formula.values())
# for element in reduce_formula.keys():
# print(len(smact.Element(element).oxidation_states), end = ",")
for i, ele_a in enumerate(list_of_elements):
paul_a = smact.Element(ele_a).pauling_eneg
for ox_a in smact.Element(ele_a).oxidation_states:
for j, ele_b in enumerate(list_of_elements[i + 1:]):
paul_b = smact.Element(ele_b).pauling_eneg
for ox_b in smact.Element(ele_b).oxidation_states:
for k, ele_c in enumerate(list_of_elements[i + j + 2:]):
paul_c = smact.Element(ele_c).pauling_eneg
for ox_c in smact.Element(ele_c).oxidation_states:
for m, ele_d in enumerate(
list_of_elements[i + j + k + 3:]):
paul_d = smact.Element(ele_d).pauling_eneg
for ox_d in smact.Element(
ele_d).oxidation_states:
for n, ele_e in enumerate(
list_of_elements[i + j + k + m +
4:]):
paul_e = smact.Element(
ele_e).pauling_eneg
for ox_e in smact.Element(
ele_e).oxidation_states:
for p, ele_f in enumerate(
list_of_elements[i + j +
k + m +
n + 5:]):
paul_f = smact.Element(
ele_f).pauling_eneg
for ox_f in smact.Element(
ele_f
).oxidation_states:
for q, ele_g in enumerate(
list_of_elements[
i + j + k + m +
n + p + 6:]):
paul_g = smact.Element(
ele_g).pauling_eneg
for ox_g in smact.Element(
ele_g
).oxidation_states:
for s, ele_h in enumerate(
list_of_elements[
i + j +
k + m +
n + p +
q +
7:]):
paul_h = smact.Element(
ele_h
).pauling_eneg
for ox_h in smact.Element(
ele_h
).oxidation_states:
# Puts elements, oxidation states and electronegativites into lists for convenience #
elements = [
ele_a,
ele_b,
ele_c,
ele_d,
ele_e,
ele_f,
ele_g,
ele_h
]
oxidation_states = [
ox_a,
ox_b,
ox_c,
ox_d,
ox_e,
ox_f,
ox_g,
ox_h
]
pauling_electro = [
paul_a,
paul_b,
paul_c,
paul_d,
paul_e,
paul_f,
paul_g,
paul_h
]
# Checks if the electronegativity makes sense and if the combination is charge neutral #
electroneg_makes_sense = pauling_test(
oxidation_states,
pauling_electro,
elements
)
cn_e, cn_r = neutral_ratios(
[
ox_a,
ox_b,
ox_c,
ox_d,
ox_e,
ox_f,
ox_g,
ox_h
],
threshold
=int(
max_num
))
if cn_e:
if electroneg_makes_sense:
pauling_count = pauling_count + 1
for num in cn_r:
if tuple(
reduce_formula
.
values(
)
) == num:
# print('{0:2s}{1:3d} {2:2s}{3:3d} {4:2s}{5:3d}'.format(ele_a, ox_a, ele_b,
# ox_b, ele_c, ox_c))
return True
print('Number of combinations = {0}'.format(pauling_count))
print("--- {0} seconds to run ---".format(time.time() - start_time))
return False
goldschmidt_ortho = []
a_too_large = []
A_B_similar = []
pauling_perov = []
anion_stats = []
for C in C_list:
anion_hex = 0
anion_cub = 0
anion_ort = 0
for B in B_list:
for A in A_list:
if B[0] != A[0]:
if C[0] != A[0] and C[0] != B[0]:
if int(A[1]) + int(B[1]) + 3 * int(C[1]) == 0:
charge_balanced.append([A[0], B[0], C[0]])
paul_a = smact.Element(A[0]).pauling_eneg
paul_b = smact.Element(B[0]).pauling_eneg
paul_c = smact.Element(C[0]).pauling_eneg
electroneg_makes_sense = screening.pauling_test(
[A[1], B[1], C[1]], [paul_a, paul_b, paul_c])
if electroneg_makes_sense:
pauling_perov.append([A[0], B[0], C[0]])
tol = (float(A[2]) + C[2]) / (np.sqrt(2) *
(float(B[2]) + C[2]))
if tol > 1.0:
a_too_large.append([A[0], B[0], C[0]])
anion_hex = anion_hex + 1
if tol > 0.9 and tol <= 1.0:
goldschmidt_cubic.append([A[0], B[0], C[0]])
anion_cub = anion_cub + 1
if tol >= 0.71 and tol < 0.9:
def test_Element_class_Pt(self):
Pt = smact.Element('Pt')
self.assertEqual(Pt.name, 'Platinum')
self.assertEqual(Pt.ionpot, 8.95883)
self.assertEqual(Pt.number, 78)
self.assertEqual(Pt.dipol, 44.00)
# ## Setting up the chemical space for the search
# Initially we define all the A elements to consider as those which have an SSE value
considered_elements = []
with open(path.join(smact.data_directory, 'SSE.csv'), 'rU') as f:
reader = csv.reader(f)
for row in reader:
considered_elements.append(row[0])
# We define a minimum SSE that the A element must have in order that it lies above the reduction potential for water splitting
SSE_min = -4.5
A_elements = []
for cation in considered_elements:
A_SSE = smact.Element(cation).SSE
if A_SSE >= SSE_min:
A_elements.append(cation)
# We define our B and C elements
B_elements = ['O', 'S', 'Se', 'Te']
C_elements = ['F', 'Cl', 'Br', 'I']
# ## Iterative search
# We now screen for possible element combinations and apply various levels of screening:
#
# 1. There must exist a charge neutral combination for some stoichiometry where x,y,z are between 1 and 8
# 2. The combination must not contravene the electronegativity rule
# 3. The predicted band gap must be between 1.5 and 2.5 eV
# 4. Environmental screening based on HHI$_R$
def compound_electroneg(verbose=False,
elements=None,
stoichs=None,
source='Mulliken'):
"""Estimate electronegativity of compound from elemental data.
Uses Mulliken electronegativity by default, which uses elemental
ionisation potentials and electron affinities. Alternatively, can
use Pauling electronegativity, re-scaled by factor 2.86 to achieve
same scale as Mulliken method (Nethercot, 1974)
DOI:10.1103/PhysRevLett.33.1088 .
Geometric mean is used (n-th root of product of components), e.g.:
X_Cu2S = (X_Cu * X_Cu * C_S)^(1/3)
Args:
elements (list) : Elements given as standard elemental symbols.
stoichs (list) : Stoichiometries, given as integers or floats.
verbose (bool) : An optional True/False flag. If True, additional information
is printed to the standard output. [Default: False]
source: String 'Mulliken' or 'Pauling'; type of Electronegativity to
use. Note that in SMACT, Pauling electronegativities are
rescaled to a Mulliken-like scale.
Returns:
Electronegativity (float) : Estimated electronegativity (no units).
"""
if type(elements[0]) == str:
elementlist = [smact.Element(i) for i in elements]
elif type(elements[0]) == smact.Element:
elementlist = elements
else:
raise Exception(
"Please supply a list of element symbols or SMACT Element objects")
stoichslist = stoichs
# Convert stoichslist from string to float
stoichslist = list(map(float, stoichslist))
# Get electronegativity values for each element
if source == 'Mulliken':
elementlist = [(el.ionpot + el.e_affinity) / 2.0 for el in elementlist]
elif source == 'Pauling':
elementlist = [(2.86 * el.pauling_eneg) for el in elementlist]
else:
raise Exception("Electronegativity type '{0}'".format(source),
"is not recognised")
# Print optional list of element electronegativities.
# This may be a useful sanity check in case of a suspicious result.
if verbose:
print("Electronegativities of elements=", elementlist)
# Raise each electronegativity to its appropriate power
# to account for stoichiometry.
for i in range(0, len(elementlist)):
elementlist[i] = [elementlist[i]**stoichslist[i]]
# Calculate geometric mean (n-th root of product)
prod = product(elementlist)
compelectroneg = (prod)**(1.0 / (sum(stoichslist)))
if verbose:
print("Geometric mean = Compound 'electronegativity'=", compelectroneg)
return compelectroneg
