class PourbaixPlotterTest(unittest.TestCase):
def setUp(self):
warnings.simplefilter("ignore")
self.test_data = loadfn(os.path.join(test_dir, "pourbaix_test_data.json"))
self.pd = PourbaixDiagram(self.test_data["Zn"])
self.plotter = PourbaixPlotter(self.pd)
def tearDown(self):
warnings.resetwarnings()
def test_plot_pourbaix(self):
plotter = PourbaixPlotter(self.pd)
# Default limits
plotter.get_pourbaix_plot()
# Non-standard limits
plotter.get_pourbaix_plot(limits=[[-5, 4], [-2, 2]])
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.test_data['Ag-Te'],
comp_dict = {"Ag": 0.5, "Te": 0.5})
binary_plotter = PourbaixPlotter(pd_binary)
test_entry = pd_binary._unprocessed_entries[0]
plt = binary_plotter.plot_entry_stability(test_entry)
plt.close()
class PourbaixPlotterTest(unittest.TestCase):
def setUp(self):
warnings.simplefilter("ignore")
self.test_data = loadfn(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"pourbaix_test_data.json"))
self.pd = PourbaixDiagram(self.test_data["Zn"])
self.plotter = PourbaixPlotter(self.pd)
def tearDown(self):
warnings.simplefilter("default")
def test_plot_pourbaix(self):
plotter = PourbaixPlotter(self.pd)
# Default limits
plotter.get_pourbaix_plot()
# Non-standard limits
plotter.get_pourbaix_plot(limits=[[-5, 4], [-2, 2]])
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.test_data["Ag-Te"],
comp_dict={
"Ag": 0.5,
"Te": 0.5
})
binary_plotter = PourbaixPlotter(pd_binary)
plt = binary_plotter.plot_entry_stability(self.test_data["Ag-Te"][53])
plt.close()
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.test_data["Ag-Te"], comp_dict={"Ag": 0.5, "Te": 0.5})
binary_plotter = PourbaixPlotter(pd_binary)
plt = binary_plotter.plot_entry_stability(self.test_data["Ag-Te"][53])
plt.close()
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.test_data['Ag-Te'],
comp_dict = {"Ag": 0.5, "Te": 0.5})
binary_plotter = PourbaixPlotter(pd_binary)
test_entry = pd_binary._unprocessed_entries[0]
plt = binary_plotter.plot_entry_stability(test_entry)
plt.close()
def pourbaix(comp, target=None, range_ph=[0, 16], range_voltage=[-2, 2]):
entries = []
try:
elements = [str(e) for e in np.unique(comp.split('-')).tolist()]
if 'O' in elements: elements.remove('O')
if 'H' in elements: elements.remove('H')
if len(elements) == 5:
print(
'2.5 milions etries will be considered. It will take more than 2 hours.'
)
'''
elif len(elements) > 6:
print('Too many etries needed to be considered. Please contact APOLEX admin ([email protected]) to perform this calculation.')
return time.strftime("%c"), -2, [0,20], [-3,3]
'''
except ValueError as e:
#print('Wrong input for the chemical space. Please put it with format "A-B-C-D"')
#return time.strftime("%c"), -1, [0,20], [-3,3]
return time.strftime(str(e)), -1, [0, 20], [-3, 3]
elements.sort()
elem = ''
for i in range(len(elements)):
elem = elem + "{}".format(elements[i])
if i + 1 == len(elements): elem = elem + ''
else: elem = elem + '-'
print(elem)
# Need to modify the directory
printtimestamp('1')
#fname = "/home/kimsooil/venv3/pourbaix/data/data_cache2/{}".format(elem)
fname = "data/data_cache2/{}".format(elem)
if os.path.isfile(fname) == True:
with open(fname, 'rb') as fr:
entries = pickle.load(fr)
print('Found it-1')
else:
try:
mpr = MPRester("8kEI0dFbzgfxX5cT")
#entries = mpr.get_pourbaix_entries(elements)
entries = getPourbaixEntryfromMongo(elements)
#print(entries)
with open(fname, 'wb') as fw:
pickle.dump(entries, fw, protocol=pickle.HIGHEST_PROTOCOL)
except ValueError as e:
if len(elements) > 4:
#return time.strftime("%c"), -2, [0,20], [-3,3]
return time.strftime(str(e)), -2, [0, 20], [-3, 3]
else:
#return time.strftime("%c"), -1, [0,20], [-3,3]
return time.strftime(str(e)), -1, [0, 20], [-3, 3]
# Need to modify the directory
#pbxname = "/home/kimsooil/venv3/pourbaix/data/data_cache2/{}-pbx".format(elem)
pbxname = "data/data_cache2/{}-pbx".format(elem)
printtimestamp('2')
if os.path.isfile(pbxname) == True:
with open(pbxname, 'rb') as pbxr:
pbx = pickle.load(pbxr)
print('Found it-2')
else:
printtimestamp('2.5')
pbx = PourbaixDiagram(entries, filter_solids=True)
with open(pbxname, 'wb') as pbxw:
pickle.dump(pbx, pbxw, protocol=pickle.HIGHEST_PROTOCOL)
printtimestamp('3')
plotter = PourbaixPlotter(pbx)
plt1 = plotter.get_pourbaix_plot(limits=[range_ph, range_voltage])
printtimestamp('4')
plt1.ylabel("E (V) vs SHE")
#plt1.title("Pourbaix diagram of {} system".format(elem+'-O-H'), fontsize=35, y=1.08)
#plt1.tight_layout()
#time_stamp = time.strftime("%c")
time_stamp = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S.%f")
plt1.savefig('static/pourbaix1_' + time_stamp + '.png')
#print(entries)
if target != None:
try:
#entry = [entry for entry in entries if Composition(entry.composition).reduced_formula == Composition(target).reduced_formula][0]#942733-LLZO Li7La3Zr2O12
entry = [entry for entry in entries if entry.name == target][0]
print(entry)
plt2 = plotter.plot_entry_stability(
entry,
pH_range=range_ph,
pH_resolution=100,
V_range=range_voltage,
V_resolution=300,
e_hull_max=1,
limits=[range_ph, range_voltage])
##plt2.tight_layout()
#plt2.title("Stability of {} in Pourbaix diagram of {} system".format(target, elem), fontsize=30, y=1.08)
plt2.ylabel("E (V) vs SHE")
plt2.savefig('static/pourbaix2_' + time_stamp + '.png')
images = 2
except:
images = 1
else:
images = 1
return time_stamp, images, range_ph, range_voltage
mpr = MPRester("6ycZ7v9nGu4TsKlA")
# Get all pourbaix entries corresponding to the Ti-Ni-O-H chemical system.
entries = mpr.get_pourbaix_entries(["Ni", "Ti"])
# Construct the PourbaixDiagram object
pbx = PourbaixDiagram(entries, comp_dict={"Ni": 0.5, "Ti": 0.5},
conc_dict={"Ni": 1e-8, "Ti": 1e-8}, filter_solids=False)
# Get an entry stability as a function of pH and V
#for e in entries:
# print(e)
entry = [e for e in entries if e.entry_id == 'ion-8'][0] #ion-8 is ti++, mp-10257 is Ni(s)
plotter = PourbaixPlotter(pbx)
bivo4_entry = [entry for entry in entries if entry.entry_id=="ion-8"][0]
plt = plotter.plot_entry_stability(bivo4_entry)
#print(pbx.get_decomposition_energy(entry, pH=0, V=-0.85))
plt.title("Ti2+ Stability Range", fontsize=50)
plt.subplots_adjust(top=0.95)
plt.tight_layout()
plt.show(figsize = (20, 15))
#plt = plotter.plot_entry_stability(entry)
with open('results/pbx_analysis.log', 'w') as f:
for idx in range(num_ini, num_fin):
formula = df_entries['formula'][idx]
mpid = df_entries['mp_id'][idx]
print('%03d_%s' % (idx + 1.0, formula))
f.writelines('%03d_%s\n' % (idx + 1.0, formula))
try:
struc = mpr.get_structure_by_material_id(mpid)
elements = [str(atom) for atom in struc.species[:2]]
entries = mpr.get_pourbaix_entries(elements)
entry_ids = [e for e in entries if e.entry_id == mpid]
if len(entry_ids) == 1:
pbx = PourbaixDiagram(entries)
plotter = PourbaixPlotter(pbx)
entry = entry_ids[0]
plt = plotter.plot_entry_stability(entry)
plt.savefig('results/plots/pourbaix/%03d_%s.png' %
(idx + 1.0, formula),
dpi=300)
elif len(entry_ids) > 1:
f.writelines('%03d_%s: number of entry > 1 \n' %
(idx + 1.0, formula))
except:
f.writelines('%03d_%s - Error: loading pourbaix entry from MP!\n' %
(idx + 1.0, formula))