def is_solid_phase(mat1, mat2, mat1_co=0.5):
"""Returns TRUE is there exists a all solid phase in the binary Pourbaix
Diagram this means that the phase doesn't have any aqueous species.
"""
mat2_co = 1 - mat1_co
pd_b = pd_entries(mat1, mat2)
pd = PourbaixDiagram(pd_b, {mat1: mat1_co, mat2: mat2_co})
pl = PourbaixPlotter(pd)
ppd = pl.pourbaix_plot_data([[-2, 16], [-3, 3]])
pd_lst = []
cnt = 0
for stable_entry in ppd[0]:
pd_lst.append([])
pd_lst[cnt].append(ppd[0][stable_entry])
pd_lst[cnt].append(stable_entry.entrylist)
cnt = cnt + 1
solidphase = False
for i in pd_lst:
if len(i[1]) == 1:
if i[1][0].phase_type == 'Solid':
solidphase = True
if len(i[1]) == 2:
if i[1][0].phase_type and i[1][1].phase_type == 'Solid':
solidphase = True
return solidphase
class TestPourbaixPlotter(unittest.TestCase):
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 tearDown(self):
warnings.resetwarnings()
def test_plot_pourbaix(self):
# Default limits
plt = self.plotter.get_pourbaix_plot()
# Non-standard limits
plt = self.plotter.get_pourbaix_plot(limits=[[-5, 4], [-2, 2]])
# Try 3-D plot
plot_3d = self.plotter._get_plot()
plot_3d_unstable = self.plotter._get_plot(label_unstable=True)
plt.close()
plot_3d.close()
plot_3d_unstable.close()
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
plt = self.plotter.plot_entry_stability(entry,
limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.multi_data['binary'],
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 TestPourbaixPlotter(unittest.TestCase):
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 test_plot_pourbaix(self):
plt = self.plotter.get_pourbaix_plot(limits=[[-2, 14], [-3, 3]])
def test_get_entry_stability(self):
entry = self.pd.all_entries[0]
plt = self.plotter.plot_entry_stability(entry,
limits=[[-2, 14], [-3, 3]])
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
plt = self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.multi_data['binary'],
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 test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
plt = self.plotter.plot_entry_stability(entry,
limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.multi_data['binary'],
comp_dict={
"Ag": 0.5,
"Te": 0.5
})
binary_plotter = PourbaixPlotter(pd_binary)
test_entry = pd_binary._unprocessed_entries[0]
binary_plotter.plot_entry_stability(test_entry)
def phase_coord(entries, atom_comp, prim_elem=False):
"""
Produces a list of line segments corresponding to each phase area in a PD
along with the PD entries corresponding to each area.
The produced list is of the following form:
list = [[[coordinate data], [pourbaix entry]], [], [] .... ]
Args:
entries: List of entries in a PD
atom_comp: Composition of atom if system is binary, given as a fraction
between 0 and 1. Corresponds to the element with lowest atomic number if
prim_elem is left to its default
prim_elem: Primary element to which the atom_comp is assigned
"""
# | - - phase_coord
from pymatgen.analysis.pourbaix.maker import PourbaixDiagram
from pymatgen.analysis.pourbaix.plotter import PourbaixPlotter
from entry_methods import base_atom
base_atoms = base_atom(entries)
mat0 = base_atoms[0]
if len(base_atoms) == 2: mat1 = base_atoms[1]
else: mat1 = mat0
# If the primary element is declared then set the given composition to it
if not prim_elem == False:
for atom in base_atoms:
if atom == prim_elem:
mat0 = atom
else:
mat1 = atom
pd = PourbaixDiagram(entries, {mat0: atom_comp, mat1: 1 - atom_comp})
pl = PourbaixPlotter(pd)
ppd = pl.pourbaix_plot_data([[-2, 16], [-3,
3]]) #ppd == Pourbaix_Plot Data
pd_lst = []
cnt = 0
for stable_entry in ppd[0]:
pd_lst.append([])
pd_lst[cnt].append(ppd[0][stable_entry])
pd_lst[cnt].append(stable_entry.entrylist)
cnt = cnt + 1
return pd_lst
def phase_coord(entries, atom_comp, prim_elem=None):
"""Produces a list of line segments corresponding to each phase area in a PD
along with the PD entries corresponding to each area.
The produced list is of the following form:
list = [[[coordinate data], [pourbaix entry]], [], [] .... ]
Parameters:
-----------
entries: list
entries in a PD
atom_comp: float
Composition of atom if system is binary, given as a fraction
between 0 and 1. Corresponds to the element with lowest atomic
number if prim_elem is left to its default
prim_elem: str
Primary element to which the atom_comp is assigned
"""
base_atoms = base_atom(entries)
mat0 = base_atoms[0]
if len(base_atoms) == 2:
mat1 = base_atoms[1]
else:
mat1 = mat0
if prim_elem:
for atom in base_atoms:
if atom == prim_elem:
mat0 = atom
else:
mat1 = atom
pd = PourbaixDiagram(entries, {mat0: atom_comp, mat1: 1 - atom_comp})
pl = PourbaixPlotter(pd)
ppd = pl.pourbaix_plot_data([[-2, 16], [-3, 3]])
pd_lst = []
for i, stable_entry in enumerate(ppd[0]):
pd_lst += [[]]
pd_lst[i] += [ppd[0][stable_entry]]
if isinstance(stable_entry, PourbaixEntry):
pd_lst[i] += [stable_entry]
else:
pd_lst[i] += [stable_entry.entrylist]
return pd_lst
def is_solid_phase(mat1, mat2, mat1_co=0.5):
"""
Returns TRUE is there exists a all solid phase in the binary Pourbaix Diagram
This means that the phase doesn't have any aqueous species
Args:
mat1:
mat2:
mat1_co:
"""
# | - - is_solid_phase
from pourdiag import pourdiag # Returns Pourbaix entries for binary system
from pymatgen.analysis.pourbaix.maker import PourbaixDiagram
from pymatgen.analysis.pourbaix.plotter import PourbaixPlotter
mat2_co = 1 - mat1_co
pd_b = pourdiag(mat1, mat2)
return pd_b
pd = PourbaixDiagram(pd_b, {mat1: mat1_co, mat2: mat2_co})
pl = PourbaixPlotter(pd)
ppd = pl.pourbaix_plot_data([[-2, 16], [-3,
3]]) #ppd == Pourbaix_Plot Data
pd_lst = []
cnt = 0
for stable_entry in ppd[0]:
pd_lst.append([])
pd_lst[cnt].append(ppd[0][stable_entry])
pd_lst[cnt].append(stable_entry.entrylist)
cnt = cnt + 1
solidphase = False
for i in pd_lst:
if len(i[1]) == 1:
if i[1][0].phase_type == 'Solid':
solidphase = True
if len(i[1]) == 2:
if i[1][0].phase_type and i[1][1].phase_type == 'Solid':
solidphase = True
return solidphase
class TestPourbaixPlotter(unittest.TestCase):
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 tearDown(self):
warnings.resetwarnings()
def test_plot_pourbaix(self):
# Default limits
plt = self.plotter.get_pourbaix_plot()
# Non-standard limits
plt = self.plotter.get_pourbaix_plot(limits=[[-5, 4], [-2, 2]])
# Try 3-D plot
plot_3d = self.plotter._get_plot()
plot_3d_unstable = self.plotter._get_plot(label_unstable=True)
plt.close()
plot_3d.close()
plot_3d_unstable.close()
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
plt = self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.multi_data['binary'],
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 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 oxidation_dissolution_product_0(i, j, scale):
"""
Creates Pourbaix Diagrams for single or binary systems
"""
#| - - oxidation_dissolution_product_0
# from pourdiag import pd_entries
from pymatgen.analysis.pourbaix.maker import PourbaixDiagram
from pymatgen.analysis.pourbaix.plotter import PourbaixPlotter
from pd_screen_tools import phase_coord, phase_filter
from stability_crit import most_stable_phase, oxidation_dissolution_product
elem0 = i.symbol; elem1 = j.symbol
mat_co_0 = 0.50 # Composition of 1st entry in elem_sys
entr = pd_entries(elem0,elem1)
pourbaix = PourbaixDiagram(entr,{elem0: mat_co_0,elem1: 1-mat_co_0})
plotter = PourbaixPlotter(pourbaix)
coord = phase_coord(entr,mat_co_0)
filt1 = phase_filter(coord,'metallic')
filt2 = phase_filter(coord,'metallic_metallic')
filt = filt1 + filt2
msp = most_stable_phase(filt,scale='RHE')
tmp = oxidation_dissolution_product(coord,msp)
if 'Ion' in tmp:
entry_lst = 'dis'
else:
entry_lst = 'oxi'
"""
entry_lst = ''
i_cnt = 0
for i in tmp:
entry_lst = str(entry_lst)+'\n'+str(i)
if i_cnt==0:
entry_lst = entry_lst[1:]
i_cnt=i_cnt+1
"""
return entry_lst
def plot_pourbaix_diagram(metastability=0.0, ion_concentration=1e-6, fmt='pdf'):
"""
Creates a Pourbaix diagram for the material in the cwd.
Args:
metastability (float): desired metastable tolerance energy
(meV/atom). <~50 is generally a sensible range to use.
ion_concentration (float): in mol/kg. Sensible values are
generally between 1e-8 and 1.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Create a ComputedEntry object for the 2D material.
composition = Structure.from_file('POSCAR').composition
energy = Vasprun('vasprun.xml').final_energy
cmpd = ComputedEntry(composition, energy)
# Define the chemsys that describes the 2D compound.
chemsys = ['O', 'H'] + [elt.symbol for elt in composition.elements
if elt.symbol not in ['O', 'H']]
# Experimental ionic energies
# See ions.yaml for ion formation energies and references.
exp_dict = ION_DATA['ExpFormEnergy']
ion_correction = ION_DATA['IonCorrection']
# Pick out the ions pertaining to the 2D compound.
ion_dict = dict()
for elt in chemsys:
if elt not in ['O', 'H'] and exp_dict[elt]:
ion_dict.update(exp_dict[elt])
elements = [Element(elt) for elt in chemsys if elt not in ['O', 'H']]
# Add "correction" for metastability
cmpd.correction -= float(cmpd.composition.num_atoms)\
* float(metastability) / 1000.0
# Calculate formation energy of the compound from its end
# members
form_energy = cmpd.energy
for elt in composition.as_dict():
form_energy -= END_MEMBERS[elt] * cmpd.composition[elt]
# Convert the compound entry to a pourbaix entry.
# Default concentration for solid entries = 1
pbx_cmpd = PourbaixEntry(cmpd)
pbx_cmpd.g0_replace(form_energy)
pbx_cmpd.reduced_entry()
# Add corrected ionic entries to the pourbaix diagram
# dft corrections for experimental ionic energies:
# Persson et.al PHYSICAL REVIEW B 85, 235438 (2012)
pbx_ion_entries = list()
# Get PourbaixEntry corresponding to each ion.
# Default concentration for ionic entries = 1e-6
# ion_energy = ion_exp_energy + ion_correction * factor
# where factor = fraction of element el in the ionic entry
# compared to the reference entry
for elt in elements:
for key in ion_dict:
comp = Ion.from_formula(key)
if comp.composition[elt] != 0:
factor = comp.composition[elt]
energy = ion_dict[key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = ion_correction[elt.symbol]\
* factor
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
# Generate and plot Pourbaix diagram
# Each bulk solid/ion has a free energy g of the form:
# g = g0_ref + 0.0591 * log10(conc) - nO * mu_H2O +
# (nH - 2nO) * pH + phi * (-nH + 2nO + q)
all_entries = [pbx_cmpd] + pbx_ion_entries
pourbaix = PourbaixDiagram(all_entries)
# Analysis features
panalyzer = PourbaixAnalyzer(pourbaix)
# instability = panalyzer.get_e_above_hull(pbx_cmpd)
plotter = PourbaixPlotter(pourbaix)
plot = plotter.get_pourbaix_plot(limits=[[0, 14], [-2, 2]],
label_domains=True)
fig = plot.gcf()
ax1 = fig.gca()
# Add coloring to highlight the stability region for the 2D
# material, if one exists.
stable_entries = plotter.pourbaix_plot_data(
limits=[[0, 14], [-2, 2]])[0]
for entry in stable_entries:
if entry == pbx_cmpd:
col = plt.cm.Blues(0)
else:
col = plt.cm.rainbow(float(
ION_COLORS[entry.composition.reduced_formula]))
vertices = plotter.domain_vertices(entry)
patch = Polygon(vertices, closed=True, fill=True, color=col)
ax1.add_patch(patch)
fig.set_size_inches((11.5, 9))
plot.tight_layout(pad=1.09)
# Save plot
if metastability:
plot.suptitle('Metastable Tolerance ='
' {} meV/atom'.format(metastability),
fontsize=20)
plot.savefig('{}_{}.{}'.format(
composition.reduced_formula, ion_concentration, fmt),
transparent=True)
else:
plot.savefig('{}_{}.{}'.format(composition.reduced_formula,
ion_concentration, fmt),
transparent=True)
plot.close()
def find_closest_point_pd(pourbaix_diagram_object):
""" """
lw = 1
limits = [[-2, 16], [-3, 3]]
plotter = PourbaixPlotter(pourbaix_diagram_object)
(stable, unstable) = plotter.pourbaix_plot_data(limits)
# Returns the Desirable Regions of PD in "vertices"
vertices = []
for entry, lines in list(stable.items()):
print(entry.name)
is_desired = screening_check_desirable(entry, criteria='only-solid')
if is_desired:
desired_entry = entry
for line in lines:
(x, y) = line
plt.plot(x, y, "k-", linewidth=lw)
point1 = [x[0], y[0]]
point2 = [x[1], y[1]]
if point1 not in vertices and is_desired:
vertices.append(point1)
if point2 not in vertices and is_desired:
vertices.append(point2)
# Placing the desired phase's name in the diagram
center_x = 0
center_y = 0
count = 0
for point in vertices:
x, y = point
count = count + 1
center_x = center_x + x
center_y = center_y + y
plt.plot(x, y, 'ro')
center_x = center_x / count
center_y = center_y / count
plt.annotate(str(desired_entry.name), xy=(center_x, center_y))
# Plotting Water and Hydrogen Equilibrium Lines. Get water line
h_line, o_line = get_water_stability_lines(limits)
plt.plot(h_line[0], h_line[1], "r--", linewidth=lw)
plt.plot(o_line[0], o_line[1], "r--", linewidth=lw)
# Getting distances
print("Getting distances of vertices")
reference_line = o_line
p1 = np.array([reference_line[0][0], reference_line[1][0]])
p2 = np.array([reference_line[0][1], reference_line[1][1]])
min_d = 1000.0
d_and_vert_lst = []
for p3 in vertices:
np.array(p3)
d = np.linalg.norm(np.cross(p2 - p1, p1 - p3)) / \
np.linalg.norm(p2 - p1)
d_and_vert = [d, p3]
d_and_vert_lst.append(d_and_vert)
# https://stackoverflow.com/questions/39840030/distance-between-point-and-a-line-from-two-points
# http://www.fundza.com/vectors/point2line/index.html
print("Vertex: ", p3, "Distance: ", d)
if d <= min_d:
min_d = d
fin_lst = []
for i in d_and_vert_lst:
if round(i[0], 4) == round(min_d, 4):
fin_lst.append(i)
# Plotting the star on highest stability vertices
for i in fin_lst:
plt.plot(i[1][0], i[1][1], '*b', ms=16)
###########################################
V_RHE = 1.23 - min_d
pH_0 = fin_lst[0][1][0]
V_SHE = V_RHE - PREFAC * pH_0
###########################################
# plt.annotate('d = '+ str(round(min_d,2)),xy=(center_x, center_y-0.3))
plt.annotate('V_crit = ' + str(round(V_RHE, 2)) +
' VvsRHE', xy=(center_x, center_y - 0.3))
plt.annotate('V_crit = ' + str(round(V_SHE, 2)) +
' VvsSHE', xy=(center_x, center_y - 0.6))
plt.xlabel("pH")
plt.ylabel("E (V)")
plt.show()
def plot_pourbaix_diagram(metastability=0.0,
ion_concentration=1e-6,
fmt='pdf'):
"""
Creates a Pourbaix diagram for the material in the cwd.
Args:
metastability (float): desired metastable tolerance energy
(meV/atom). <~50 is generally a sensible range to use.
ion_concentration (float): in mol/kg. Sensible values are
generally between 1e-8 and 1.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Create a ComputedEntry object for the 2D material.
composition = Structure.from_file('POSCAR').composition
energy = Vasprun('vasprun.xml').final_energy
cmpd = ComputedEntry(composition, energy)
# Define the chemsys that describes the 2D compound.
chemsys = ['O', 'H'] + [
elt.symbol
for elt in composition.elements if elt.symbol not in ['O', 'H']
]
# Pick out the ions pertaining to the 2D compound.
ion_dict = dict()
for elt in chemsys:
if elt not in ['O', 'H'] and ION_FORMATION_ENERGIES[elt]:
ion_dict.update(ION_FORMATION_ENERGIES[elt])
elements = [Element(elt) for elt in chemsys if elt not in ['O', 'H']]
# Add "correction" for metastability
cmpd.correction -= float(cmpd.composition.num_atoms)\
* float(metastability) / 1000.0
# Calculate formation energy of the compound from its end
# members
form_energy = cmpd.energy
for elt in composition.as_dict():
form_energy -= CHEMICAL_POTENTIALS[elt] * cmpd.composition[elt]
# Convert the compound entry to a pourbaix entry.
# Default concentration for solid entries = 1
pbx_cmpd = PourbaixEntry(cmpd)
pbx_cmpd.g0_replace(form_energy)
pbx_cmpd.reduced_entry()
# Add corrected ionic entries to the pourbaix diagram
# dft corrections for experimental ionic energies:
# Persson et.al PHYSICAL REVIEW B 85, 235438 (2012)
pbx_ion_entries = list()
# Get PourbaixEntry corresponding to each ion.
# Default concentration for ionic entries = 1e-6
# ion_energy = ion_exp_energy + ion_correction * factor
# where factor = fraction of element el in the ionic entry
# compared to the reference entry
for elt in elements:
for key in ion_dict:
comp = Ion.from_formula(key)
if comp.composition[elt] != 0:
factor = comp.composition[elt]
energy = ion_dict[key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = (ION_CORRECTIONS[elt.symbol] *
factor)
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
# Generate and plot Pourbaix diagram
# Each bulk solid/ion has a free energy g of the form:
# g = g0_ref + 0.0591 * log10(conc) - nO * mu_H2O +
# (nH - 2nO) * pH + phi * (-nH + 2nO + q)
all_entries = [pbx_cmpd] + pbx_ion_entries
pourbaix = PourbaixDiagram(all_entries)
# Analysis features
# panalyzer = PourbaixAnalyzer(pourbaix)
# instability = panalyzer.get_e_above_hull(pbx_cmpd)
plotter = PourbaixPlotter(pourbaix)
plot = plotter.get_pourbaix_plot(limits=[[0, 14], [-2, 2]],
label_domains=True)
fig = plot.gcf()
ax1 = fig.gca()
# Add coloring to highlight the stability region for the 2D
# material, if one exists.
stable_entries = plotter.pourbaix_plot_data(limits=[[0, 14], [-2, 2]])[0]
for entry in stable_entries:
if entry == pbx_cmpd:
col = plt.cm.Blues(0)
else:
col = plt.cm.rainbow(
float(ION_COLORS[entry.composition.reduced_formula]))
vertices = plotter.domain_vertices(entry)
patch = Polygon(vertices, closed=True, fill=True, color=col)
ax1.add_patch(patch)
fig.set_size_inches((11.5, 9))
plot.tight_layout(pad=1.09)
# Save plot
if metastability:
plot.suptitle('Metastable Tolerance ='
' {} meV/atom'.format(metastability),
fontsize=20)
plot.savefig('{}_{}.{}'.format(composition.reduced_formula,
ion_concentration, fmt),
transparent=True)
else:
plot.savefig('{}_{}.{}'.format(composition.reduced_formula,
ion_concentration, fmt),
transparent=True)
plot.close()
def find_closest_point_pd(pourbaix_diagram_object):
from pymatgen.analysis.pourbaix.plotter import PourbaixPlotter
import matplotlib.pyplot as plt
import numpy as np
from pymatgen.util.coord_utils import in_coord_list
from pymatgen.analysis.pourbaix.maker import PREFAC
lw = 1
limits = [[-2, 16], [-3, 3]]
fig1 = plt.figure()
ax = fig1.gca()
plotter = PourbaixPlotter(pourbaix_diagram_object)
(stable, unstable) = plotter.pourbaix_plot_data(limits)
#| - - Ambar's Region Filter Check Function
def screening_check_desirable(entry, criteria='only-solid'):
is_desired = False
if criteria not in ['only-solid']:
print "Not implemented"
sys.exit()
if criteria == 'only-solid':
if entry.nH2O == 0.0 and entry.npH == 0.0 and entry.nPhi == 0.0:
is_desired = True
print "Desired entry", entry.name
if not criteria:
print "Not desired entry", entry.name
return is_desired
#__|
#| - - Ambar's Function for Water and Hydrogen Lines
def get_water_stability_lines(limits):
from pymatgen.analysis.pourbaix.maker import PREFAC
xlim = limits[0]
ylim = limits[1]
h_line = np.transpose([[xlim[0], -xlim[0] * PREFAC],
[xlim[1], -xlim[1] * PREFAC]])
o_line = np.transpose([[xlim[0], -xlim[0] * PREFAC + 1.23],
[xlim[1], -xlim[1] * PREFAC + 1.23]])
return (h_line, o_line)
#__|
#| - - Returns the Desirable Regions of PD in "vertices"
vertices = []
import time
for entry, lines in stable.items():
print entry.name
is_desired = screening_check_desirable(entry, criteria='only-solid')
if is_desired:
desired_entry = entry
for line in lines:
(x, y) = line
#print "points", x, y
plt.plot(x, y, "k-", linewidth=lw)
point1 = [x[0], y[0]]
point2 = [x[1], y[1]]
if point1 not in vertices and is_desired:
vertices.append(point1)
if point2 not in vertices and is_desired:
vertices.append(point2)
#__|
#| - - Placing the desired phase's name in the diagram
center_x = 0
center_y = 0
count = 0
for point in vertices:
x, y = point
count = count + 1
center_x = center_x + x
center_y = center_y + y
plt.plot(x, y, 'ro')
center_x = center_x / count
center_y = center_y / count
plt.annotate(str(desired_entry.name), xy=(center_x, center_y))
#__|
#| - - Plotting Water and Hydrogen Equilibrium Lines
# Get water line
h_line, o_line = get_water_stability_lines(limits)
plt.plot(h_line[0], h_line[1], "r--", linewidth=lw)
plt.plot(o_line[0], o_line[1], "r--", linewidth=lw)
#__|
# Getting distances
print "Getting distances of vertices"
reference_line = o_line
p1 = np.array([reference_line[0][0], reference_line[1][0]])
p2 = np.array([reference_line[0][1], reference_line[1][1]])
min_d = 1000.0
min_vertex = []
d_and_vert_lst = []
for p3 in vertices:
np.array(p3)
d = np.linalg.norm(np.cross(p2 - p1,
p1 - p3)) / np.linalg.norm(p2 - p1)
d_and_vert = [d, p3]
d_and_vert_lst.append(d_and_vert)
#https://stackoverflow.com/questions/39840030/distance-between-point-and-a-line-from-two-points
#http://www.fundza.com/vectors/point2line/index.html
print "Vertex: ", p3, "Distance: ", d
if d <= min_d:
min_d = d
min_vertex = p3
fin_lst = []
for i in d_and_vert_lst:
if round(i[0], 4) == round(min_d, 4):
fin_lst.append(i)
# Plotting the star on highest stability vertices
for i in fin_lst:
plt.plot(i[1][0], i[1][1], '*b', ms=16)
###########################################
V_RHE = 1.23 - min_d
pH_0 = fin_lst[0][1][0]
V_SHE = V_RHE - PREFAC * pH_0
###########################################
# plt.annotate('d = '+ str(round(min_d,2)),xy=(center_x, center_y-0.3))
plt.annotate('V_crit = ' + str(round(V_RHE, 2)) + ' VvsRHE',
xy=(center_x, center_y - 0.3))
plt.annotate('V_crit = ' + str(round(V_SHE, 2)) + ' VvsSHE',
xy=(center_x, center_y - 0.6))
plt.xlabel("pH")
plt.ylabel("E (V)")
plt.show()
def plot_pourbaix_diagram(metastability=0.0, ion_concentration=1e-6, fmt='pdf'):
"""
Creates a Pourbaix diagram for the material in the cwd.
Args:
metastability (float): desired metastable tolerance energy
(meV/atom). <~50 is generally a sensible range to use.
ion_concentration (float): in mol/kg. Sensible values are
generally between 1e-8 and 1.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Create a ComputedEntry object for the 2D material.
composition = Structure.from_file('POSCAR').composition
energy = Vasprun('vasprun.xml').final_energy
cmpd = ComputedEntry(composition, energy)
# Define the chemsys that describes the 2D compound.
chemsys = ['O', 'H'] + [elt.symbol for elt in composition.elements
if elt.symbol not in ['O', 'H']]
# Pick out the ions pertaining to the 2D compound.
ion_dict = dict()
for elt in chemsys:
if elt not in ['O', 'H'] and ION_FORMATION_ENERGIES[elt]:
ion_dict.update(ION_FORMATION_ENERGIES[elt])
elements = [Element(elt) for elt in chemsys if elt not in ['O', 'H']]
# Add "correction" for metastability
cmpd.correction -= float(cmpd.composition.num_atoms)\
* float(metastability) / 1000.0
# Calculate formation energy of the compound from its end
# members
form_energy = cmpd.energy
for elt in composition.as_dict():
form_energy -= CHEMICAL_POTENTIALS[elt] * cmpd.composition[elt]
# Convert the compound entry to a pourbaix entry.
# Default concentration for solid entries = 1
pbx_cmpd = PourbaixEntry(cmpd)
pbx_cmpd.g0_replace(form_energy)
pbx_cmpd.reduced_entry()
# Add corrected ionic entries to the pourbaix diagram
# dft corrections for experimental ionic energies:
# Persson et.al PHYSICAL REVIEW B 85, 235438 (2012)
pbx_ion_entries = list()
# Get PourbaixEntry corresponding to each ion.
# Default concentration for ionic entries = 1e-6
# ion_energy = ion_exp_energy + ion_correction * factor
# where factor = fraction of element el in the ionic entry
# compared to the reference entry
for elt in elements:
for key in ion_dict:
comp = Ion.from_formula(key)
if comp.composition[elt] != 0:
factor = comp.composition[elt]
energy = ion_dict[key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = (
ION_CORRECTIONS[elt.symbol] * factor
)
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
# Generate and plot Pourbaix diagram
# Each bulk solid/ion has a free energy g of the form:
# g = g0_ref + 0.0591 * log10(conc) - nO * mu_H2O +
# (nH - 2nO) * pH + phi * (-nH + 2nO + q)
all_entries = [pbx_cmpd] + pbx_ion_entries
total = sum([composition[el] for el in elements])
comp_dict = {el.symbol: composition[el]/total for el in elements}
pourbaix_diagram = PourbaixDiagram(all_entries, comp_dict=comp_dict)
plotter = PourbaixPlotter(pourbaix_diagram)
# Plotting details...
font = "serif"
fig = plt.figure(figsize=(14, 9))
ax1 = fig.gca()
ax1.set_xlim([0, 14])
ax1.set_xticklabels([int(t) for t in ax1.get_xticks()], fontname=font,
fontsize=18)
ax1.set_ylim(-2, 2)
ax1.set_yticklabels(ax1.get_yticks(), fontname=font, fontsize=18)
ax1.set_xlabel("pH", fontname=font, fontsize=18)
ax1.set_ylabel("Potential vs. SHE (V)", fontname=font, fontsize=18)
# Outline water's stability range.
ax1.plot([0, 14], [0, -0.829], color="gray", linestyle="--", alpha=0.7,
linewidth=2)
ax1.plot([0, 14], [1.229, 0.401], color="gray", linestyle="--", alpha=0.7,
linewidth=2)
stable_entries = plotter.pourbaix_plot_data(
limits=[[0, 14], [-2, 2]])[0]
# Add coloring.
colors = sb.color_palette("Set2", len(stable_entries))
i = 0
for entry in stable_entries:
col = colors[i]
i += 1
vertices = plotter.domain_vertices(entry)
center_x = sum([v[0] for v in vertices])/len(vertices)
center_y = sum([v[1] for v in vertices])/len(vertices)
patch = Polygon(vertices, closed=True, fill=True, facecolor=col,
linewidth=2, edgecolor="w")
ax1.text(center_x, center_y, plotter.print_name(entry),
verticalalignment="center", horizontalalignment="center",
fontname=font, fontsize=18)
ax1.add_patch(patch)
plt.savefig("pourbaix.{}".format(fmt))
plt.close()
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)
