def get_tote(structure_type, form_e, species, oxides_table_path, debug=False):
# formula = spe2form(structure_type, species)
# composition = Composition(formula)
spe_dict = Counter({})
for site in SITE_INFO[structure_type]:
spe_dict += Counter({spe.__str__(): round(SITE_INFO[structure_type][site]['num_atoms'] \
* species[site][spe]) \
for spe in sorted(species[site], key=lambda x: species[site][x])})
composition = Composition(spe_dict)
tote = form_e
for el, amt in composition.items():
if debug:
print(el)
stable_ox_entry = None
if el.symbol == 'O':
continue
if el.symbol in BINARY_OXDIES_ENTRIES:
stable_ox_entry = BINARY_OXDIES_ENTRIES[el.symbol]
if not stable_ox_entry:
stable_ox_table = loadfn(oxides_table_path)
stable_ox_id = stable_ox_table[el.__str__()]['mpid']
stable_ox_entry = m.get_entry_by_material_id(
stable_ox_id,
property_data=['e_above_hull', 'formation_energy_per_atom'])
min_e = stable_ox_entry.uncorrected_energy
amt_ox = stable_ox_entry.composition[el.name]
tote += (amt / amt_ox) * min_e
return tote
def parse_formula(formula, max_len=9):
f = Composition(formula).fractional_composition.as_dict()
matrix = np.zeros((max_len, len(elements)))
for i, ent in enumerate(f.items()):
el, num = ent
el = elements.index(el)
matrix[i, el] = num
# matrix[i, -1] = num / total
return matrix
def get_tote(structure_type, form_e, species, debug=False):
spe_dict = Counter({})
for site in SITE_INFO[structure_type]:
spe_dict += Counter({spe.__str__(): round(SITE_INFO[structure_type][site]['num_atoms'] \
* species[site][spe]) \
for spe in sorted(species[site], key=lambda x: species[site][x])})
composition = Composition(spe_dict)
tote = form_e
for el, amt in composition.items():
if debug:
print(el)
if el.symbol == 'O':
continue
if BINARY_OXDIES_ENTRIES.get(el.__str__()):
stable_ox_entry = BINARY_OXDIES_ENTRIES[el.__str__()]
else:
raise ValueError("No binary oxide entry for %s" % el.__str__())
min_e = stable_ox_entry.uncorrected_energy
amt_ox = stable_ox_entry.composition[el.name]
tote += (amt / amt_ox) * min_e
return tote
def parse_composition(structure_type, s, ctype):
toks = s.strip().split()
if len(toks) == 1:
c = Composition({toks[0].split(":")[0]: 1})
else:
c = Composition(
{t.split(":")[0]: float(t.split(":")[1])
for t in toks})
c = Composition({k2: v2 / sum(c.values()) for k2, v2 in c.items()})
if len(c) != 2:
raise ValueError("Bad composition on %s." % ctype)
frac = [c.get_atomic_fraction(k) for k in c.keys()]
if structure_type == 'garnet':
if ctype == "A":
if abs(frac[0] - 0.5) > 0.01:
raise ValueError("Bad composition on %s. "
"Only 1:1 mixing allowed!" % ctype)
elif ctype in ["C", "D"]:
if not (abs(frac[0] - 1.0 / 3) < 0.01
or abs(frac[1] - 1.0 / 3) < 0.01):
raise ValueError("Bad composition on %s. "
"Only 2:1 mixing allowed!" % ctype)
elif structure_type == 'perovskite':
if abs(frac[0] - 0.5) > 0.01:
raise ValueError("Bad composition on %s. "
"Only 1:1 mixing allowed!" % ctype)
try:
for k in c.keys():
k.oxi_state
if k not in ELS[structure_type][ctype]:
raise ValueError("%s is not a valid species for %s site." %
(k, ctype))
except AttributeError:
raise ValueError("Oxidation states must be specified for all species!")
return c
def formula_to_periodic_table(self):
def channel(x, y):
'''
x: horizontal
y: vertical
'''
# f 14, d 10, p 6
x, y = x + 1, y + 1 # changing to start from 1. 1 is the origin
if y == 1 or x <= 2:
channel = 0 # s
elif 27 <= x:
channel = 1 # p
elif x == 3 or (3 + 14 + 1 <= x and x <= 17 + 9):
channel = 2 # d
elif 4 <= x and x <= 17:
channel = 3 # f
else:
print("error in making channel in period_table_as_img")
return channel
dict_formula = Composition(self.formula).as_dict()
coordinate = np.zeros([4, 7, 18 + 14], dtype=np.float32)
for key, value in dict_formula.items():
i = self.allowed_elements_list.index(key)
# print(key)
num = i + 1 # which is element number as H of num is 1
# 18+14=32 # channel mens s,p,d, and f
if num == 1: # H
coordinate[channel(0, 0), 0, 0] = value
elif num == 2: # He
coordinate[channel(0, 32 - 1), 0, 32 - 1] = value
elif num <= 18:
# if q, mod=divmod(10,3) then q=3, mod=1
y, x = divmod(num - 2, 8)
if x == 1 or x == 2:
coordinate[channel(y + 1, x - 1), y + 1, x - 1] = value
else:
if x == 0:
x = 8
y -= 1
x = x + 10 + 14
coordinate[channel(y + 1, x - 1), y + 1, x - 1] = value
elif num <= 54: # from K to Xe, which are from 4th and 5th period
y, x = divmod(num - 18, 18)
if x == 0:
x = 18
y -= 1
if x == 1 or x == 2 or x == 3:
coordinate[channel(y + 3, x - 1), y + 3, x - 1] = value
else:
x = x + 14
coordinate[channel(y + 3, x - 1), y + 3, x - 1] = value
elif num <= 118:
y, x = divmod(num - 54, 32)
if x == 0:
x = 32
y -= 1
coordinate[channel(y + 5, x - 1), y + 5, x - 1] = value
else:
raise ValueError('error in period to image-like')
# dict[key] = coordinate
# if 'Tl' in dict.keys():
# dict['TI'] = dict['Tl']
# if 'Li' in dict.keys():
# dict['LI'] = dict['Li']
return coordinate
