def to_csv(self, filename: str, latexify_names: bool = False):
"""
Exports PDEntries to a csv
Args:
filename: Filename to write to.
entries: PDEntries to export.
latexify_names: Format entry names to be LaTex compatible,
e.g., Li_{2}O
"""
elements = set()
for entry in self.entries:
elements.update(entry.composition.elements)
elements = sorted(list(elements), key=lambda a: a.X)
writer = csv.writer(open(filename, "w"),
delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
writer.writerow(["Name"] + elements + ["Energy"])
for entry in self.entries:
row = [
entry.name if not latexify_names else re.sub(
r"([0-9]+)", r"_{\1}", entry.name)
]
row.extend([entry.composition[el] for el in elements])
row.append(entry.energy)
writer.writerow(row)
def from_csv(cls, filename: str):
"""
Imports PDEntries from a csv.
Args:
filename: Filename to import from.
Returns:
List of Elements, List of PDEntries
"""
with open(filename, "r", encoding="utf-8") as f:
reader = csv.reader(f,
delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
entries = list()
header_read = False
elements = None
for row in reader:
if not header_read:
elements = row[1:(len(row) - 1)]
header_read = True
else:
name = row[0]
energy = float(row[-1])
comp = dict()
for ind in range(1, len(row) - 1):
if float(row[ind]) > 0:
comp[Element(elements[ind - 1])] = float(row[ind])
entries.append(PDEntry(Composition(comp), energy, name))
return cls(entries)
def to_csv(filename, entries, latexify_names=False):
"""
Exports Pourbaix entries to a csv
Args:
filename: Filename to write to.
entries: Entries to export.
latexify_names: Format entry names to be LaTex compatible, e.g.,
Li_{2}O
"""
elements = set()
# TODO: oh god please fix this next line
list(map(elements.update, [entry.entry.composition.elements for entry in entries]))
elements = sorted(list(elements), key=lambda a: a.X)
with open(filename, "w") as f:
writer = csv.writer(f, delimiter=unicode2str(","), quotechar=unicode2str('"'), quoting=csv.QUOTE_MINIMAL)
writer.writerow(["Name"] + elements + ["Energy"] + ["Entry Type"] + ["Charge"] + ["Concentration"])
for entry in entries:
row = [entry.name if not latexify_names else re.sub(r"([0-9]+)", r"_{\1}", entry.name)]
if entry.phase_type == "Solid":
reduction_fac = entry.entry.composition.get_reduced_composition_and_factor()[1]
else:
reduction_fac = 1.0
row.extend([entry.entry.composition[el] / reduction_fac for el in elements])
if entry.phase_type == "Solid":
reduction_fac = 1.0
row.append(entry.g0 / reduction_fac)
row.append(entry.phase_type)
row.append(entry.charge / reduction_fac)
row.append(entry.conc)
writer.writerow(row)
def from_csv(filename):
"""
Imports PDEntries from a csv.
Args:
filename: Filename to import from.
Returns:
List of Elements, List of PDEntries
"""
with open(filename, "r", encoding="utf-8") as f:
reader = csv.reader(f, delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
entries = list()
header_read = False
for row in reader:
if not header_read:
elements = row[1:(len(row) - 1)]
header_read = True
else:
name = row[0]
energy = float(row[-1])
comp = dict()
for ind in range(1, len(row) - 1):
if float(row[ind]) > 0:
comp[Element(elements[ind - 1])] = float(row[ind])
entries.append(PDEntry(Composition(comp), energy, name))
elements = [Element(el) for el in elements]
return elements, entries
def to_csv(filename, entries, latexify_names=False):
"""
Exports PDEntries to a csv
Args:
filename: Filename to write to.
entries: PDEntries to export.
latexify_names: Format entry names to be LaTex compatible,
e.g., Li_{2}O
"""
import csv
elements = set()
for entry in entries:
elements.update(entry.composition.elements)
elements = sorted(list(elements), key=lambda a: a.X)
writer = csv.writer(open(filename, "wb"), delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
writer.writerow(["Name"] + elements + ["Energy"])
for entry in entries:
row = [entry.name if not latexify_names
else re.sub(r"([0-9]+)", r"_{\1}", entry.name)]
row.extend([entry.composition[el] for el in elements])
row.append(entry.energy)
writer.writerow(row)
def to_csv(filename, entries, latexify_names=False):
"""
Exports Pourbaix entries to a csv
Args:
filename: Filename to write to.
entries: Entries to export.
latexify_names: Format entry names to be LaTex compatible, e.g.,
Li_{2}O
"""
elements = set()
#TODO: oh god please fix this next line
list(
map(elements.update,
[entry.entry.composition.elements for entry in entries]))
elements = sorted(list(elements), key=lambda a: a.X)
with open(filename, "w") as f:
writer = csv.writer(f,
delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
writer.writerow(["Name"] + elements + ["Energy"] + ["Entry Type"] +
["Charge"] + ["Concentration"])
for entry in entries:
row = [
entry.name if not latexify_names else re.sub(
r"([0-9]+)", r"_{\1}", entry.name)
]
if entry.phase_type == "Solid":
reduction_fac = entry.entry.composition.\
get_reduced_composition_and_factor()[1]
else:
reduction_fac = 1.0
row.extend([
entry.entry.composition[el] / reduction_fac
for el in elements
])
if entry.phase_type == "Solid":
reduction_fac = 1.0
row.append(entry.g0 / reduction_fac)
row.append(entry.phase_type)
row.append(entry.charge / reduction_fac)
row.append(entry.conc)
writer.writerow(row)
def __init__(self, filename):
# read in data from file
self._chemsys_entries = defaultdict(list)
filename = os.path.join(os.path.dirname(__file__), filename)
reader = csv.reader(open(filename, "rt"), quotechar=unicode2str("|"))
for row in reader:
comp = Composition(row[0])
cost_per_mol = float(row[1]) * comp.weight.to("kg") * AVOGADROS_CONST
pde = CostEntry(comp.formula, cost_per_mol, row[2], row[3])
chemsys = "-".join(sorted([el.symbol for el in pde.composition.elements]))
self._chemsys_entries[chemsys].append(pde)
def from_csv(filename):
"""
Imports PourbaixEntries from a csv.
Args:
filename: Filename to import from.
Returns:
List of Entries
"""
with open(filename, "r") as f:
reader = csv.reader(f,
delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
entries = list()
header_read = False
for row in reader:
if not header_read:
elements = row[1:(len(row) - 4)]
header_read = True
else:
name = row[0]
energy = float(row[-4])
conc = float(row[-1])
comp = dict()
for ind in range(1, len(row) - 4):
if float(row[ind]) > 0:
comp[Element(elements[ind - 1])] = float(row[ind])
phase_type = row[-3]
if phase_type == "Ion":
PoE = PourbaixEntry(
IonEntry(Ion.from_formula(name), energy))
PoE.conc = conc
PoE.name = name
entries.append(PoE)
else:
entries.append(
PourbaixEntry(PDEntry(Composition(comp), energy)))
elements = [Element(el) for el in elements]
return elements, entries
def __init__(self, filename):
# read in data from file
self._chemsys_entries = defaultdict(list)
filename = os.path.join(os.path.dirname(__file__), filename)
reader = csv.reader(open(filename, "rt"), quotechar=unicode2str("|"))
for row in reader:
comp = Composition(row[0])
cost_per_mol = float(row[1]) * comp.weight.to("kg") * const.N_A
pde = CostEntry(comp.formula, cost_per_mol, row[2], row[3])
chemsys = "-".join(
sorted([el.symbol for el in pde.composition.elements]))
self._chemsys_entries[chemsys].append(pde)
def from_csv(filename):
"""
Imports PourbaixEntries from a csv.
Args:
filename: Filename to import from.
Returns:
List of Entries
"""
with open(filename, "r") as f:
reader = csv.reader(f, delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
entries = list()
header_read = False
for row in reader:
if not header_read:
elements = row[1:(len(row) - 4)]
header_read = True
else:
name = row[0]
energy = float(row[-4])
conc = float(row[-1])
comp = dict()
for ind in range(1, len(row) - 4):
if float(row[ind]) > 0:
comp[Element(elements[ind - 1])] = float(row[ind])
phase_type = row[-3]
if phase_type == "Ion":
PoE = PourbaixEntry(IonEntry(Ion.from_formula(name),
energy))
PoE.conc = conc
PoE.name = name
entries.append(PoE)
else:
entries.append(PourbaixEntry(PDEntry(Composition(comp),
energy)))
elements = [Element(el) for el in elements]
return elements, entries
def test_unicode2str(self):
if sys.version_info.major < 3:
self.assertEqual(type(unicode2str("a")), str)
else:
self.assertEqual(type(unicode2str("a")), str)
def test_unicode2str(self):
if sys.version_info.major < 3:
self.assertEqual(type(unicode2str("a")), str)
else:
self.assertEqual(type(unicode2str("a")), str)