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 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
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]])
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter
# %matplotlib inline
# Initialize the MP Rester
mpr = MPRester("hvSDrzMafUtXE0JQ") ##将API 秘钥输入适配器中，并且初始化适配器，需要自己申请。
# Get all pourbaix entries corresponding to the Cu-O-H chemical system.
entries = mpr.get_pourbaix_entries(["Cu"])
# Construct the PourbaixDiagram object
pbx = PourbaixDiagram(entries)
# Get an entry stability as a function of pH and V
entry = [e for e in entries if e.entry_id == 'mp-1692'][0]
print(
"CuO's potential energy per atom relative to the most",
"stable decomposition product is {:0.2f} eV/atom".format(
pbx.get_decomposition_energy(entry, pH=7, V=-0.2)))
plotter = PourbaixPlotter(pbx)
plotter.get_pourbaix_plot().show()
plt = plotter.plot_entry_stability(entry)
plt.show()
# Get all pourbaix entries corresponding to the Fe-O-H chemical system.
entries = mpr.get_pourbaix_entries(["Bi", "V"])
# Construct the PourbaixDiagram object
pbx = PourbaixDiagram(entries,
comp_dict={
"Bi": 0.5,
"V": 0.5
},
conc_dict={
"Bi": 1e-8,
"V": 1e-8
},
filter_solids=True)