def read(cls, doscar='', efermi=0.0):
print(doscar)
if Path(doscar[0:(len(doscar)-7)]+'/pbe_bands/vasprun.xml' ).is_file():
try:
band_structure = Vasprun(doscar[0:(len(doscar)-7)]+'/pbe_bands/vasprun.xml').get_band_structure()
dos = DOS(file=doscar)
dos._efermi = 0.0
dos.read_doscar(dos.file)
dos.efermi = band_structure.efermi
gap = band_structure.get_band_gap()
dos.gap = gap['energy']
dos.is_directBG = gap['direct']
except ValueError:
raise simulation.analysis.vasp.calculation.VaspError('Could not parse DOSCAR')
return dos
elif Path(doscar[0:(len(doscar)-7)]+'/hse_bands/vasprun.xml' ).is_file():
try:
band_structure = Vasprun(doscar[0:(len(doscar)-7)]+'/hse_bands/vasprun.xml').get_band_structure()
dos = DOS(file=doscar)
dos._efermi = 0.0
dos.read_doscar(dos.file)
dos.efermi = band_structure.efermi
gap = band_structure.get_band_gap()
dos.gap = gap['energy']
dos.is_directBG = gap['direct']
except ValueError:
raise simulation.analysis.vasp.calculation.VaspError('Could not parse DOSCAR')
return dos
else:
try:
band_structure = Vasprun(doscar[0:(len(doscar) - 7)] + '/vasprun.xml').get_band_structure()
dos = DOS(file=doscar)
dos._efermi = 0.0
dos.read_doscar(dos.file)
dos.efermi = band_structure.efermi
gap = band_structure.get_band_gap()
dos.gap = gap['energy']
dos.is_directBG = gap['direct']
except ValueError:
raise simulation.analysis.vasp.calculation.VaspError('Could not parse DOSCAR')
return dos
def plot_band_alignments(directories, run_type='PBE', fmt='pdf'):
"""
Plot CBM's and VBM's of all compounds together, relative to the band
edges of H2O.
Args:
directories (list): list of the directory paths for materials
to include in the plot.
run_type (str): 'PBE' or 'HSE', so that the function knows which
subdirectory to go into (pbe_bands or hse_bands).
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
if run_type == 'HSE':
subdirectory = 'hse_bands'
else:
subdirectory = 'pbe_bands'
band_gaps = {}
for directory in directories:
sub_dir = os.path.join(directory, subdirectory)
if is_converged(sub_dir):
os.chdir(sub_dir)
band_structure = Vasprun('vasprun.xml').get_band_structure()
band_gap = band_structure.get_band_gap()
# Vacuum level energy from LOCPOT.
locpot = Locpot.from_file('LOCPOT')
evac = max(locpot.get_average_along_axis(2))
if not band_structure.is_metal():
is_direct = band_gap['direct']
cbm = band_structure.get_cbm()
vbm = band_structure.get_vbm()
else:
cbm = None
vbm = None
is_direct = False
band_gaps[directory] = {'CBM': cbm, 'VBM': vbm,
'Direct': is_direct,
'Metal': band_structure.is_metal(),
'E_vac': evac}
os.chdir('../../')
ax = plt.figure(figsize=(16, 10)).gca()
x_max = len(band_gaps) * 1.315
ax.set_xlim(0, x_max)
# Rectangle representing band edges of water.
ax.add_patch(plt.Rectangle((0, -5.67), height=1.23, width=len(band_gaps),
facecolor='#00cc99', linewidth=0))
ax.text(len(band_gaps) * 1.01, -4.44, r'$\mathrm{H+/H_2}$', size=20,
verticalalignment='center')
ax.text(len(band_gaps) * 1.01, -5.67, r'$\mathrm{O_2/H_2O}$', size=20,
verticalalignment='center')
x_ticklabels = []
y_min = -8
i = 0
# Nothing but lies.
are_directs, are_indirects, are_metals = False, False, False
for compound in [cpd for cpd in directories if cpd in band_gaps]:
x_ticklabels.append(compound)
# Plot all energies relative to their vacuum level.
evac = band_gaps[compound]['E_vac']
if band_gaps[compound]['Metal']:
cbm = -8
vbm = -2
else:
cbm = band_gaps[compound]['CBM']['energy'] - evac
vbm = band_gaps[compound]['VBM']['energy'] - evac
# Add a box around direct gap compounds to distinguish them.
if band_gaps[compound]['Direct']:
are_directs = True
linewidth = 5
elif not band_gaps[compound]['Metal']:
are_indirects = True
linewidth = 0
# Metals are grey.
if band_gaps[compound]['Metal']:
are_metals = True
linewidth = 0
color_code = '#404040'
else:
color_code = '#002b80'
# CBM
ax.add_patch(plt.Rectangle((i, cbm), height=-cbm, width=0.8,
facecolor=color_code, linewidth=linewidth,
edgecolor="#e68a00"))
# VBM
ax.add_patch(plt.Rectangle((i, y_min),
height=(vbm - y_min), width=0.8,
facecolor=color_code, linewidth=linewidth,
edgecolor="#e68a00"))
i += 1
ax.set_ylim(y_min, 0)
# Set tick labels
ax.set_xticks([n + 0.4 for n in range(i)])
ax.set_xticklabels(x_ticklabels, family='serif', size=20, rotation=60)
ax.set_yticklabels(ax.get_yticks(), family='serif', size=20)
# Add a legend
height = y_min
if are_directs:
ax.add_patch(plt.Rectangle((i*1.165, height), width=i*0.15,
height=(-y_min*0.1), facecolor='#002b80',
edgecolor='#e68a00', linewidth=5))
ax.text(i*1.24, height - y_min * 0.05, 'Direct', family='serif',
color='w', size=20, horizontalalignment='center',
verticalalignment='center')
height -= y_min * 0.15
if are_indirects:
ax.add_patch(plt.Rectangle((i*1.165, height), width=i*0.15,
height=(-y_min*0.1), facecolor='#002b80',
linewidth=0))
ax.text(i*1.24, height - y_min * 0.05, 'Indirect', family='serif',
size=20, color='w', horizontalalignment='center',
verticalalignment='center')
height -= y_min * 0.15
if are_metals:
ax.add_patch(plt.Rectangle((i*1.165, height), width=i*0.15,
height=(-y_min*0.1), facecolor='#404040',
linewidth=0))
ax.text(i*1.24, height - y_min * 0.05, 'Metal', family='serif',
size=20, color='w', horizontalalignment='center',
verticalalignment='center')
# Who needs axes?
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
ax.set_ylabel('eV', family='serif', size=24)
if fmt == "None":
return ax
else:
plt.savefig('band_alignments.{}'.format(fmt), transparent=True)
plt.close()
def plot_band_alignments(directories, run_type='PBE', fmt='pdf'):
"""
Plot CBM's and VBM's of all compounds together, relative to the band
edges of H2O.
Args:
directories (list): list of the directory paths for materials
to include in the plot.
run_type (str): 'PBE' or 'HSE', so that the function knows which
subdirectory to go into (pbe_bands or hse_bands).
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
if run_type == 'HSE':
subdirectory = 'hse_bands'
else:
subdirectory = 'pbe_bands'
band_gaps = {}
for directory in directories:
sub_dir = os.path.join(directory, subdirectory)
if is_converged(sub_dir):
os.chdir(sub_dir)
band_structure = Vasprun('vasprun.xml').get_band_structure()
band_gap = band_structure.get_band_gap()
# Vacuum level energy from LOCPOT.
locpot = Locpot.from_file('LOCPOT')
evac = max(locpot.get_average_along_axis(2))
if not band_structure.is_metal():
is_direct = band_gap['direct']
cbm = band_structure.get_cbm()
vbm = band_structure.get_vbm()
else:
cbm = None
vbm = None
is_direct = False
band_gaps[directory] = {
'CBM': cbm,
'VBM': vbm,
'Direct': is_direct,
'Metal': band_structure.is_metal(),
'E_vac': evac
}
os.chdir('../../')
ax = plt.figure(figsize=(16, 10)).gca()
x_max = len(band_gaps) * 1.315
ax.set_xlim(0, x_max)
# Rectangle representing band edges of water.
ax.add_patch(
plt.Rectangle((0, -5.67),
height=1.23,
width=len(band_gaps),
facecolor='#00cc99',
linewidth=0))
ax.text(len(band_gaps) * 1.01,
-4.44,
r'$\mathrm{H+/H_2}$',
size=20,
verticalalignment='center')
ax.text(len(band_gaps) * 1.01,
-5.67,
r'$\mathrm{O_2/H_2O}$',
size=20,
verticalalignment='center')
x_ticklabels = []
y_min = -8
i = 0
# Nothing but lies.
are_directs, are_indirects, are_metals = False, False, False
for compound in [cpd for cpd in directories if cpd in band_gaps]:
x_ticklabels.append(compound)
# Plot all energies relative to their vacuum level.
evac = band_gaps[compound]['E_vac']
if band_gaps[compound]['Metal']:
cbm = -8
vbm = -2
else:
cbm = band_gaps[compound]['CBM']['energy'] - evac
vbm = band_gaps[compound]['VBM']['energy'] - evac
# Add a box around direct gap compounds to distinguish them.
if band_gaps[compound]['Direct']:
are_directs = True
linewidth = 5
elif not band_gaps[compound]['Metal']:
are_indirects = True
linewidth = 0
# Metals are grey.
if band_gaps[compound]['Metal']:
are_metals = True
linewidth = 0
color_code = '#404040'
else:
color_code = '#002b80'
# CBM
ax.add_patch(
plt.Rectangle((i, cbm),
height=-cbm,
width=0.8,
facecolor=color_code,
linewidth=linewidth,
edgecolor="#e68a00"))
# VBM
ax.add_patch(
plt.Rectangle((i, y_min),
height=(vbm - y_min),
width=0.8,
facecolor=color_code,
linewidth=linewidth,
edgecolor="#e68a00"))
i += 1
ax.set_ylim(y_min, 0)
# Set tick labels
ax.set_xticks([n + 0.4 for n in range(i)])
ax.set_xticklabels(x_ticklabels, family='serif', size=20, rotation=60)
ax.set_yticklabels(ax.get_yticks(), family='serif', size=20)
# Add a legend
height = y_min
if are_directs:
ax.add_patch(
plt.Rectangle((i * 1.165, height),
width=i * 0.15,
height=(-y_min * 0.1),
facecolor='#002b80',
edgecolor='#e68a00',
linewidth=5))
ax.text(i * 1.24,
height - y_min * 0.05,
'Direct',
family='serif',
color='w',
size=20,
horizontalalignment='center',
verticalalignment='center')
height -= y_min * 0.15
if are_indirects:
ax.add_patch(
plt.Rectangle((i * 1.165, height),
width=i * 0.15,
height=(-y_min * 0.1),
facecolor='#002b80',
linewidth=0))
ax.text(i * 1.24,
height - y_min * 0.05,
'Indirect',
family='serif',
size=20,
color='w',
horizontalalignment='center',
verticalalignment='center')
height -= y_min * 0.15
if are_metals:
ax.add_patch(
plt.Rectangle((i * 1.165, height),
width=i * 0.15,
height=(-y_min * 0.1),
facecolor='#404040',
linewidth=0))
ax.text(i * 1.24,
height - y_min * 0.05,
'Metal',
family='serif',
size=20,
color='w',
horizontalalignment='center',
verticalalignment='center')
# Who needs axes?
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_ticks_position('bottom')
ax.set_ylabel('eV', family='serif', size=24)
if fmt == "None":
return ax
else:
plt.savefig('band_alignments.{}'.format(fmt), transparent=True)
plt.close()
def plot_band_alignments(directories, run_type="PBE", fmt="pdf"):
"""
Plot CBM's and VBM's of all compounds together, relative to the band
edges of H2O.
Args:
directories (list): list of the directory paths for materials
to include in the plot.
run_type (str): 'PBE' or 'HSE', so that the function knows which
subdirectory to go into (pbe_bands or hse_bands).
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
if run_type == "HSE":
subdirectory = "hse_bands"
else:
subdirectory = "pbe_bands"
band_gaps = {}
for directory in directories:
if is_converged("{}/{}".format(directory, subdirectory)):
os.chdir("{}/{}".format(directory, subdirectory))
band_structure = Vasprun("vasprun.xml").get_band_structure()
band_gap = band_structure.get_band_gap()
# Vacuum level energy from LOCPOT.
locpot = Locpot.from_file("LOCPOT")
evac = max(locpot.get_average_along_axis(2))
try:
is_metal = False
is_direct = band_gap["direct"]
cbm = band_structure.get_cbm()
vbm = band_structure.get_vbm()
except AttributeError:
cbm = None
vbm = None
is_metal = True
is_direct = False
band_gaps[directory] = {"CBM": cbm, "VBM": vbm, "Direct": is_direct, "Metal": is_metal, "E_vac": evac}
os.chdir("../../")
ax = plt.figure(figsize=(16, 10)).gca()
x_max = len(band_gaps) * 1.315
ax.set_xlim(0, x_max)
# Rectangle representing band edges of water.
ax.add_patch(plt.Rectangle((0, -5.67), height=1.23, width=len(band_gaps), facecolor="#00cc99", linewidth=0))
ax.text(len(band_gaps) * 1.01, -4.44, r"$\mathrm{H+/H_2}$", size=20, verticalalignment="center")
ax.text(len(band_gaps) * 1.01, -5.67, r"$\mathrm{O_2/H_2O}$", size=20, verticalalignment="center")
x_ticklabels = []
y_min = -8
i = 0
# Nothing but lies.
are_directs, are_indirects, are_metals = False, False, False
for compound in [cpd for cpd in directories if cpd in band_gaps]:
x_ticklabels.append(compound)
# Plot all energies relative to their vacuum level.
evac = band_gaps[compound]["E_vac"]
if band_gaps[compound]["Metal"]:
cbm = -8
vbm = -2
else:
cbm = band_gaps[compound]["CBM"]["energy"] - evac
vbm = band_gaps[compound]["VBM"]["energy"] - evac
# Add a box around direct gap compounds to distinguish them.
if band_gaps[compound]["Direct"]:
are_directs = True
linewidth = 5
elif not band_gaps[compound]["Metal"]:
are_indirects = True
linewidth = 0
# Metals are grey.
if band_gaps[compound]["Metal"]:
are_metals = True
linewidth = 0
color_code = "#404040"
else:
color_code = "#002b80"
# CBM
ax.add_patch(
plt.Rectangle(
(i, cbm), height=-cbm, width=0.8, facecolor=color_code, linewidth=linewidth, edgecolor="#e68a00"
)
)
# VBM
ax.add_patch(
plt.Rectangle(
(i, y_min),
height=(vbm - y_min),
width=0.8,
facecolor=color_code,
linewidth=linewidth,
edgecolor="#e68a00",
)
)
i += 1
ax.set_ylim(y_min, -2)
# Set tick labels
ax.set_xticks([n + 0.4 for n in range(i)])
ax.set_xticklabels(x_ticklabels, family="serif", size=20, rotation=60)
ax.set_yticklabels(ax.get_yticks(), family="serif", size=20)
# Add a legend
height = y_min
if are_directs:
ax.add_patch(
plt.Rectangle(
(i * 1.165, height),
width=i * 0.15,
height=(-y_min * 0.1),
facecolor="#002b80",
edgecolor="#e68a00",
linewidth=5,
)
)
ax.text(
i * 1.24,
height - y_min * 0.05,
"Direct",
family="serif",
color="w",
size=20,
horizontalalignment="center",
verticalalignment="center",
)
height -= y_min * 0.15
if are_indirects:
ax.add_patch(
plt.Rectangle((i * 1.165, height), width=i * 0.15, height=(-y_min * 0.1), facecolor="#002b80", linewidth=0)
)
ax.text(
i * 1.24,
height - y_min * 0.05,
"Indirect",
family="serif",
size=20,
color="w",
horizontalalignment="center",
verticalalignment="center",
)
height -= y_min * 0.15
if are_metals:
ax.add_patch(
plt.Rectangle((i * 1.165, height), width=i * 0.15, height=(-y_min * 0.1), facecolor="#404040", linewidth=0)
)
ax.text(
i * 1.24,
height - y_min * 0.05,
"Metal",
family="serif",
size=20,
color="w",
horizontalalignment="center",
verticalalignment="center",
)
# Who needs axes?
ax.spines["top"].set_visible(False)
ax.spines["right"].set_visible(False)
ax.spines["bottom"].set_visible(False)
ax.spines["left"].set_visible(False)
ax.yaxis.set_ticks_position("left")
ax.xaxis.set_ticks_position("bottom")
ax.set_ylabel("eV", family="serif", size=24)
plt.savefig("band_alignments.{}".format(fmt), transparent=True)
plt.close()
