def test_read_write_csv(self):
Zn_solids = ["Zn", "ZnO", "ZnO2"]
sol_g = [0.0, -3.338, -1.315]
Zn_ions = ["Zn[2+]", "ZnOH[+]", "HZnO2[-]", "ZnO2[2-]", "ZnO"]
liq_g = [-1.527, -3.415, -4.812, -4.036, -2.921]
liq_conc = [1e-6, 1e-6, 1e-6, 1e-6, 1e-6]
solid_entry = list()
for sol in Zn_solids:
comp = Composition(sol)
delg = sol_g[Zn_solids.index(sol)]
solid_entry.append(PourbaixEntry(PDEntry(comp, delg)))
ion_entry = list()
for ion in Zn_ions:
comp_ion = Ion.from_formula(ion)
delg = liq_g[Zn_ions.index(ion)]
conc = liq_conc[Zn_ions.index(ion)]
PoE = PourbaixEntry(IonEntry(comp_ion, delg))
PoE.set_conc(conc)
ion_entry.append(PoE)
entries = solid_entry + ion_entry
PourbaixEntryIO.to_csv("pourbaix_test_entries.csv", entries)
(elements, entries) = PourbaixEntryIO.from_csv(
"pourbaix_test_entries.csv")
self.assertEqual(elements,
[Element('Zn'), Element('H'), Element('O')],
"Wrong elements!")
self.assertEqual(len(entries), 8, "Wrong number of entries!")
os.remove("pourbaix_test_entries.csv")
def test_read_write_csv(self):
Zn_solids = ["Zn", "ZnO", "ZnO2"]
sol_g = [0.0, -3.338, -1.315]
Zn_ions = ["Zn[2+]", "ZnOH[+]", "HZnO2[-]", "ZnO2[2-]", "ZnO"]
liq_g = [-1.527, -3.415, -4.812, -4.036, -2.921]
liq_conc = [1e-6, 1e-6, 1e-6, 1e-6, 1e-6]
solid_entry = list()
for sol in Zn_solids:
comp = Composition(sol)
delg = sol_g[Zn_solids.index(sol)]
solid_entry.append(PourbaixEntry(PDEntry(comp, delg)))
ion_entry = list()
for ion in Zn_ions:
comp_ion = Ion.from_formula(ion)
delg = liq_g[Zn_ions.index(ion)]
conc = liq_conc[Zn_ions.index(ion)]
PoE = PourbaixEntry(IonEntry(comp_ion, delg))
PoE.conc = conc
ion_entry.append(PoE)
entries = solid_entry + ion_entry
PourbaixEntryIO.to_csv("pourbaix_test_entries.csv", entries)
(elements,
entries) = PourbaixEntryIO.from_csv("pourbaix_test_entries.csv")
self.assertEqual(
elements, [Element('Zn'),
Element('H'), Element('O')], "Wrong elements!")
self.assertEqual(len(entries), 8, "Wrong number of entries!")
os.remove("pourbaix_test_entries.csv")
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(
os.path.join(module_dir, "test_entries.csv"))
self.num_simplices = {
"Zn(s)": 7,
"ZnO2(s)": 7,
"Zn[2+]": 4,
"ZnO2[2-]": 4,
"ZnHO2[-]": 4
}
self.e_above_hull_test = {"ZnHO[+]": 0.0693, "ZnO(aq)": 0.0624}
self.decomp_test = {
"ZnHO[+]": {
"ZnO(s)": 0.5,
"Zn[2+]": 0.5
},
"ZnO(aq)": {
"ZnO(s)": 1.0
}
}
self.pd = PourbaixDiagram(entries)
self.analyzer = PourbaixAnalyzer(self.pd)
self.multi_data = loadfn(os.path.join(test_dir, 'multicomp_pbx.json'))
warnings.simplefilter("ignore")
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(os.path.join(module_dir,
"test_entries.csv"))
self._entries = entries
self._pd = PourbaixDiagram(entries)
self.list_of_stable_entries = ["ZnO(s)", "Zn[2+]", "ZnO2(s)", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)"]
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(
os.path.join(module_dir, "test_entries.csv"))
self._entries = entries
self._pd = PourbaixDiagram(entries)
self.list_of_stable_entries = [
"ZnO(s)", "Zn[2+]", "ZnO2(s)", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)"
]
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(os.path.join(module_dir,
"test_entries.csv"))
self.num_simplices = {"Zn(s)": 7, "ZnO2(s)": 7, "Zn[2+]": 4, "ZnO2[2-]": 4, "ZnHO2[-]": 4}
self.e_above_hull_test = {"ZnHO[+]": 0.0693, "ZnO(aq)": 0.0624}
self.decomp_test = {"ZnHO[+]": {"ZnO(s)": 0.5, "Zn[2+]": 0.5}, "ZnO(aq)": {"ZnO(s)": 1.0}}
self.pd = PourbaixDiagram(entries)
self.analyzer = PourbaixAnalyzer(self.pd)
def setUp(self):
warnings.simplefilter("ignore")
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(os.path.join(module_dir,
"test_entries.csv"))
self.num_simplices = {"Zn(s)": 7, "ZnO2(s)": 7, "Zn[2+]": 4, "ZnO2[2-]": 4, "ZnHO2[-]": 4}
self.e_above_hull_test = {"ZnHO[+]": 0.0693, "ZnO(aq)": 0.0624}
self.decomp_test = {"ZnHO[+]": {"ZnO(s)": 0.5, "Zn[2+]": 0.5}, "ZnO(aq)": {"ZnO(s)": 1.0}}
self.pd = PourbaixDiagram(entries)
self.multi_data = loadfn(os.path.join(test_dir, 'multicomp_pbx.json'))
self.plotter = PourbaixPlotter(self.pd)
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(
os.path.join(module_dir, "test_entries.csv"))
self.num_simplices = {
"Zn(s)": 7,
"ZnO2(s)": 7,
"Zn[2+]": 4,
"ZnO2[2-]": 4,
"ZnHO2[-]": 4
}
self.e_above_hull_test = {"ZnHO[+]": 0.0693, "ZnO(aq)": 0.0624}
self.decomp_test = {
"ZnHO[+]": {
"ZnO(s)": 0.5,
"Zn[2+]": 0.5
},
"ZnO(aq)": {
"ZnO(s)": 1.0
}
}
self.pd = PourbaixDiagram(entries)
self.plotter = PourbaixPlotter(self.pd)
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(
os.path.join(module_dir, "test_entries.csv"))
self._entries = entries
self._pd = PourbaixDiagram(entries)
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(elements, entries) = PourbaixEntryIO.from_csv(os.path.join(module_dir,
"test_entries.csv"))
self._entries = entries
self._pd = PourbaixDiagram(entries)
Created on Wed Feb 28 15:40:02 2018
@author: jherfson
"""
from pymatgen.analysis.pourbaix.entry import PourbaixEntry, IonEntry #, MultiEntry
from pymatgen.analysis.pourbaix.entry import PourbaixEntryIO
from pymatgen.analysis.phase_diagram import PDEntry
from pymatgen.core.ion import Ion
from pymatgen.core.structure import Composition
Zn_solids = ["Zn", "ZnO", "ZnO2"]
sol_g = [0.0, -3.338, -1.315]
Zn_ions = ["Zn[2+]", "ZnOH[+]", "HZnO2[-]", "ZnO2[2-]", "ZnO"]
liq_g = [-1.527, -3.415, -4.812, -4.036, -2.921]
liq_conc = [1e-6, 1e-6, 1e-6, 1e-6, 1e-6]
solid_entry = list()
for sol in Zn_solids:
comp = Composition(sol)
delg = sol_g[Zn_solids.index(sol)]
solid_entry.append(PourbaixEntry(PDEntry(comp, delg)))
ion_entry = list()
for ion in Zn_ions:
comp_ion = Ion.from_formula(ion)
delg = liq_g[Zn_ions.index(ion)]
conc = liq_conc[Zn_ions.index(ion)]
PoE = PourbaixEntry(IonEntry(comp_ion, delg))
PoE.conc = conc
ion_entry.append(PoE)
entries = solid_entry + ion_entry
PourbaixEntryIO.to_csv("pourbaix_test_entries.csv", entries)