def get_decomposed_entries(structure_type, species, oxides_table_path):
"""
Get decomposed entries for mix types
Args:one
species (dict): species in dictionary.
structure_type(str): garnet or perovskite
Returns:
decompose entries(list):
list of entries prepared from unmix
garnets/perovskite decomposed from input mix
garnet/perovskite
"""
def decomposed(specie_complex):
"""Decompose those have sub-dict to individual dict objects."""
for site, specie in specie_complex.items():
spe_copy = specie_complex.copy()
if len(specie) > 1:
for spe, amt in specie.items():
spe_copy[site] = {spe: 1}
yield spe_copy
decompose_entries = []
model, scaler, graph = load_model_and_scaler(structure_type, "unmix")
std_formula = STD_FORMULA[structure_type]
for unmix_species in decomposed(species):
charge = sum([
spe.oxi_state * amt * SITE_INFO[structure_type][site]["num_atoms"]
for site in SITE_INFO[structure_type].keys()
for spe, amt in unmix_species[site].items()
])
if not abs(charge - 2 * std_formula['O']) < 0.1:
continue
formula = spe2form(structure_type, unmix_species)
calc_entries = [entry for entry in CALC_ENTRIES[structure_type] if \
entry.name == Composition(formula).reduced_formula]
if calc_entries:
for entry in calc_entries:
decompose_entries.append(entry)
else:
descriptors = get_descriptor(structure_type, unmix_species)
with graph.as_default():
form_e = get_form_e(descriptors, model, scaler)
# tot_e = get_tote(form_e * std_formula.num_atoms, unmix_species)
tot_e = get_tote(structure_type, form_e * std_formula.num_atoms,
unmix_species, oxides_table_path)
entry = prepare_entry(structure_type, tot_e, unmix_species)
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
decompose_entries.append(entry)
return decompose_entries
def get_decomposed_entries(structure_type, species):
"""
Get decomposed entries for mix types
Args:
structure_type(str): "garnet" or "perovskite"
species (dict): species in dictionary.
structure_type(str): garnet or perovskite
Returns:
decompose entries(list):
list of entries prepared from unmix
garnets/perovskite decomposed from input mix
garnet/perovskite
"""
def decomposed(specie_complex):
"""Decompose those have sub-dict to individual dict objects."""
for site, specie in specie_complex.items():
spe_copy = specie_complex.copy()
if len(specie) > 1:
for spe, amt in specie.items():
spe_copy[site] = {spe: 1}
yield spe_copy
decompose_entries = []
model, scaler = load_model_and_scaler(structure_type, "unmix")
std_formula = STD_FORMULA[structure_type]
for unmix_species in decomposed(species):
charge = sum([
spe.oxi_state * amt * SITE_INFO[structure_type][site]["num_atoms"]
for site in SITE_INFO[structure_type].keys()
for spe, amt in unmix_species[site].items()
])
if not abs(charge - 2 * std_formula['O']) < 0.1:
continue
formula = spe2form(structure_type, unmix_species)
composition = Composition(formula)
elements = [el.name for el in composition]
chemsy = '-'.join(sorted(elements))
calc_entries = []
if CALC_ENTRIES[structure_type].get(chemsy):
calc_entries = [entry for entry in CALC_ENTRIES[structure_type][chemsy] if \
entry.name == Composition(formula).reduced_formula]
else:
pass
if calc_entries:
decompose_entries.extend(calc_entries)
else:
cn_specific = True if structure_type == 'garnet' else False
descriptors = get_descriptor(structure_type,
unmix_species,
cn_specific=cn_specific)
form_e = get_form_e(descriptors, model, scaler)
# tot_e = get_tote(form_e * std_formula.num_atoms, unmix_species)
tot_e = get_tote(structure_type, form_e * std_formula.num_atoms,
unmix_species)
entry = prepare_entry(structure_type, tot_e, unmix_species)
compat = MaterialsProjectCompatibility()
entry = compat.process_entry(entry)
decompose_entries.append(entry)
return decompose_entries
def query():
try:
structure_type = 'garnet'
c_string = request.args.get("c_string")
a_string = request.args.get("a_string")
d_string = request.args.get("d_string")
formula = ""
c_composition = parse_composition(structure_type, c_string, "C")
a_composition = parse_composition(structure_type, a_string, "A")
d_composition = parse_composition(structure_type, d_string, "D")
charge = -2.0 * 12
for k in c_composition.keys():
charge += 3 * k.oxi_state * c_composition.get_atomic_fraction(k)
for k in a_composition.keys():
charge += 2 * k.oxi_state * a_composition.get_atomic_fraction(k)
for k in d_composition.keys():
charge += 3 * k.oxi_state * d_composition.get_atomic_fraction(k)
if len(c_composition) > 1:
mix_site = "c"
elif len(a_composition) > 1:
mix_site = "a"
elif len(d_composition) > 1:
mix_site = "d"
else:
mix_site = None
species = {"a": a_composition, "d": d_composition, "c": c_composition}
if abs(charge) < 0.1:
formula = spe2form(structure_type, species)
if ResponseCache.get(formula):
response = ResponseCache[formula]
form_e = response['form_e']
decomp = response['decomp']
ehull = response['ehull']
else: # Cache miss
with tf.Session() as sess:
model, scaler, graph = load_model_and_scaler(structure_type, mix_site) if mix_site \
else load_model_and_scaler(structure_type, "unmix")
inputs = get_descriptor(structure_type, species)
with graph.as_default():
form_e = get_form_e(inputs, model, scaler) * 20
tot_e = get_tote(structure_type, form_e, species)
if mix_site:
decompose_entries = get_decomposed_entries(
structure_type, species)
decomp, ehull = get_ehull(
structure_type,
tot_e,
species,
unmix_entries=decompose_entries)
else:
decomp, ehull = get_ehull(structure_type, tot_e,
species)
response = {"form_e": form_e, "decomp": decomp, "ehull": ehull}
if len(ResponseCache) > MAX_CACHE:
ResponseCache.popitem(last=False)
ResponseCache.update({formula: response})
message = [
"<i>E<sub>f</sub></i> = %.3f eV/fu" % form_e,
"<i>E<sub>hull</sub></i> = %.0f meV/atom" % (ehull * 1000)
]
if ehull > 0:
reaction = []
for k, v in decomp.items():
comp = k.composition
comp, f = comp.get_reduced_composition_and_factor()
reaction.append(
'%.3f <a href="https://www.materialsproject.org/materials/%s">%s</a>'
% (v * f / comp.num_atoms * 20, k.entry_id,
html_formula(comp.reduced_formula)))
message.append("Decomposition: " + " + ".join(reaction))
message = "<br>".join(message)
else:
message = "Not charge neutral! Total charge = %.0f" % charge
except Exception as ex:
message = str(ex)
return make_response(
render_template('index.html',
c_string=c_string,
a_string=a_string,
d_string=d_string,
formula=html_formula(formula),
message=message))
def perovskite_query():
try:
structure_type = 'perovskite'
a_string = request.args.get("a_string")
b_string = request.args.get("b_string")
formula = ""
a_composition = parse_composition(structure_type, a_string, "A")
b_composition = parse_composition(structure_type, b_string, "B")
charge = -2.0 * 6
for k in a_composition.keys():
charge += 2 * k.oxi_state * a_composition.get_atomic_fraction(k)
for k in b_composition.keys():
charge += 2 * k.oxi_state * b_composition.get_atomic_fraction(k)
if len(a_composition) > 1:
mix_site = "a"
elif len(b_composition) > 1:
mix_site = "b"
else:
mix_site = None
species = {"a": a_composition, "b": b_composition}
if abs(charge) < 0.1:
formula = spe2form(structure_type, species)
if ResponseCache.get(formula):
response = ResponseCache[formula]
form_e = response['form_e']
decomp = response['decomp']
ehull = response['ehull']
else: # Cache miss
with tf.Session() as sess:
model, scaler, graph = load_model_and_scaler(structure_type, mix_site) if mix_site \
else load_model_and_scaler(structure_type, "unmix")
inputs = get_descriptor(structure_type,
species,
cn_specific=False)
with graph.as_default():
form_e = get_form_e(inputs, model, scaler) * 10
# form_e predicted from model is always in /atom
# the get_tote func always returns the tote with in /standard fu
# which is A2B2O6, 10 atoms
tot_e = get_tote(structure_type, form_e, species)
if mix_site:
decompose_entries = get_decomposed_entries(
structure_type, species)
decomp, ehull = get_ehull(
structure_type,
tot_e,
species,
unmix_entries=decompose_entries)
else:
decomp, ehull = get_ehull(structure_type, tot_e,
species)
response = {
"form_e": form_e,
"decomp": decomp,
"ehull": ehull
}
if len(ResponseCache) > MAX_CACHE:
ResponseCache.popitem(last=False)
ResponseCache.update({formula: response})
message = [
"<i>E<sub>f</sub></i> = %.3f eV/fu" % (form_e),
"<i>E<sub>hull</sub></i> = %.0f meV/atom" % (ehull * 1000)
]
if ehull > 0:
reaction = []
for k, v in decomp.items():
comp = k.composition
rcomp, f = comp.get_reduced_composition_and_factor()
reaction.append(
'%.3f <a href="https://www.materialsproject.org/materials/%s">%s</a>'
% (v * f / comp.num_atoms * 10, k.entry_id,
html_formula(comp.reduced_formula)))
message.append("Decomposition: " + " + ".join(reaction))
message = "<br>".join(message)
else:
message = "Not charge neutral! Total charge = %.0f" % charge
except Exception as ex:
message = str(ex)
return make_response(
render_template('index_perov.html',
a_string=a_string,
b_string=b_string,
formula=html_formula(formula),
message=message))
def query(nclicks, c_string, a_string, d_string):
if nclicks > 0:
try:
structure_type = 'garnet'
formula = ""
c_composition = parse_composition(structure_type, c_string, "C")
a_composition = parse_composition(structure_type, a_string, "A")
d_composition = parse_composition(structure_type, d_string, "D")
charge = -2.0 * 12
for k in c_composition.keys():
charge += 3 * k.oxi_state * c_composition.get_atomic_fraction(k)
for k in a_composition.keys():
charge += 2 * k.oxi_state * a_composition.get_atomic_fraction(k)
for k in d_composition.keys():
charge += 3 * k.oxi_state * d_composition.get_atomic_fraction(k)
if len(c_composition) > 1:
mix_site = "c"
elif len(a_composition) > 1:
mix_site = "a"
elif len(d_composition) > 1:
mix_site = "d"
else:
mix_site = None
species = {"a": a_composition, "d": d_composition, "c": c_composition}
if abs(charge) < 0.1:
with tf.Session() as sess:
oxide_table_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"data/garnet_oxi_table.json")
model, scaler, graph = load_model_and_scaler(structure_type, mix_site) if mix_site \
else load_model_and_scaler(structure_type, "unmix")
inputs = get_descriptor(structure_type, species)
with graph.as_default():
form_e = get_form_e(inputs, model, scaler) * 20
tot_e = get_tote(structure_type, form_e, species,
oxides_table_path=oxide_table_path)
if mix_site:
decompose_entries = get_decomposed_entries(structure_type,
species,
oxide_table_path)
decomp, ehull = get_ehull(structure_type, tot_e, species,
unmix_entries=decompose_entries)
else:
decomp, ehull = get_ehull(structure_type, tot_e, species)
formula = spe2form(structure_type, species)
message = [html.P("Ef = %.3f eV/fu" % form_e),
html.P("Ehull = %.0f meV/atom" % (ehull * 1000))]
if ehull > 0:
message.append(html.Span("Decomposition: "))
i = 0
for k, v in decomp.items():
comp = k.composition
comp, f = comp.get_reduced_composition_and_factor()
if i != 0:
message.append(html.Span(" + "))
message.append(html.Span("%.3f" % (v * f / comp.num_atoms * 20)))
message.append(dcc.Link(comp.reduced_formula,
href='https://www.materialsproject.org/materials/%s' % k.entry_id)
)
i += 1
else:
message = [html.P("Not charge neutral! Total charge = %.0f" % charge)]
except Exception as ex:
message = html.P(str(ex))
print(message)
return message