def test_mpr_pipeline(self):
from pymatgen import MPRester
mpr = MPRester()
data = mpr.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = mpr.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data,
filter_solids=True,
conc_dict={
"Ag": 1e-8,
"Te": 1e-8
})
self.assertEqual(len(pbx.stable_entries), 30)
test_entry = pbx.find_stable_entry(8, 2)
self.assertAlmostEqual(test_entry.energy, 2.3936747835000016, 3)
# Test custom ions
entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
custom_ion_entry = PourbaixEntry(ion, entry_id='my_ion')
pbx = PourbaixDiagram(entries + [custom_ion_entry],
filter_solids=True,
comp_dict={
"Na": 1,
"Sn": 12,
"C": 24
})
self.assertAlmostEqual(
pbx.get_decomposition_energy(custom_ion_entry, 5, 2),
8.31202738629504, 2)
def test_heavy(self):
from pymatgen import MPRester
mpr = MPRester()
entries = mpr.get_pourbaix_entries(["Li", "Mg", "Sn", "Pd"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = mpr.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = mpr.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F", "Fe"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = mpr.get_pourbaix_entries(["Na", "Ca", "Nd", "Y", "Ho", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
def test_mpr_pipeline(self):
from pymatgen import MPRester
mpr = MPRester()
data = mpr.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = mpr.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data,
filter_solids=True,
conc_dict={
"Ag": 1e-8,
"Te": 1e-8
})
self.assertEqual(len(pbx.stable_entries), 30)
test_entry = pbx.find_stable_entry(8, 2)
self.assertAlmostEqual(test_entry.energy, 2.3894017960000009, 1)
# Test custom ions
entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
custom_ion_entry = PourbaixEntry(ion, entry_id='my_ion')
pbx = PourbaixDiagram(entries + [custom_ion_entry],
filter_solids=True,
comp_dict={
"Na": 1,
"Sn": 12,
"C": 24
})
self.assertAlmostEqual(
pbx.get_decomposition_energy(custom_ion_entry, 5, 2), 2.1209002582,
1)
# Test against ion sets with multiple equivalent ions (Bi-V regression)
entries = mpr.get_pourbaix_entries(["Bi", "V"])
pbx = PourbaixDiagram(entries,
filter_solids=True,
conc_dict={
"Bi": 1e-8,
"V": 1e-8
})
self.assertTrue(
all([
'Bi' in entry.composition and 'V' in entry.composition
for entry in pbx.all_entries
]))
def test_mpr_pipeline(self):
from pymatgen import MPRester
mpr = MPRester()
data = mpr.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = mpr.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data, filter_solids=True,
conc_dict={"Ag": 1e-8, "Te": 1e-8})
self.assertEqual(len(pbx.stable_entries), 30)
test_entry = pbx.find_stable_entry(8, 2)
self.assertAlmostEqual(test_entry.energy, 2.393900378500001)
# Test custom ions
entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
custom_ion_entry = PourbaixEntry(ion, entry_id='my_ion')
pbx = PourbaixDiagram(entries + [custom_ion_entry], filter_solids=True,
comp_dict={"Na": 1, "Sn": 12, "C": 24})
self.assertAlmostEqual(pbx.get_decomposition_energy(custom_ion_entry, 5, 2),
8.31082110278154)
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 19 20:21:39 2018
@author: Jeran
"""
from pymatgen import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter
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)
# !/usr/bin/env python
# -*- coding:utf-8 -*-
# author:春梅
# Import necessary tools from pymatgen
from pymatgen import MPRester
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
},
# | - Script Inputs
#This initializes the REST adaptor. Put your own API key in.
path_i = os.path.join(os.environ["PROJ_irox"], "config", "config.yml")
with open(path_i) as file:
config_dict = yaml.load(file, Loader=yaml.FullLoader)
api_key = config_dict["materials_project"]["api_key"]
mpr = MPRester(api_key) # Raul
#__|
# -
entries = mpr.get_pourbaix_entries(
[
"Ir",
]
)
entry = entries[0]
entry.uncorrected_energy
# entry
# Pourbaix Entry : Ir1 O4 with energy = 7.4405, npH = -8.0, nPhi = -7.0, nH2O = 4.0, entry_id = None
assert False
# + jupyter={}
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))
