def relax(dim=2, submit=True, force_overwrite=False):
"""
Writes input files and (optionally) submits a self-consistent
relaxation. Should be run before pretty much anything else, in
order to get the right energy and structure of the material.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
if force_overwrite or not utl.is_converged(os.getcwd()):
directory = os.getcwd().split('/')[-1]
# vdw_kernel.bindat file required for VDW calculations.
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
# KPOINTS
Kpoints.automatic_density(Structure.from_file('POSCAR'),
1000).write_file('KPOINTS')
# INCAR
INCAR_DICT.update(
{'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))}
)
Incar.from_dict(INCAR_DICT).write_file('INCAR')
# POTCAR
utl.write_potcar()
# Special tasks only performed for 2D materials.
if dim == 2:
# Ensure 20A interlayer vacuum
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
# Remove all z k-points.
kpts_lines = open('KPOINTS').readlines()
with open('KPOINTS', 'w') as kpts:
for line in kpts_lines[:3]:
kpts.write(line)
kpts.write(kpts_lines[3].split()[0] + ' '
+ kpts_lines[3].split()[1] + ' 1')
# Submission script
if dim == 2:
binary = VASP_TWOD_BIN
elif dim == 3:
binary = VASP_STD_BIN
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
def relax(dim=2, submit=True, force_overwrite=False):
"""
Writes input files and (optionally) submits a self-consistent
relaxation. Should be run before pretty much anything else, in
order to get the right energy and structure of the material.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
if force_overwrite or not utl.is_converged(os.getcwd()):
directory = os.getcwd().split('/')[-1]
# vdw_kernel.bindat file required for VDW calculations.
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
# KPOINTS
Kpoints.automatic_density(Structure.from_file('POSCAR'),
1000).write_file('KPOINTS')
# INCAR
INCAR_DICT.update(
{'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(INCAR_DICT).write_file('INCAR')
# POTCAR
utl.write_potcar()
# Special tasks only performed for 2D materials.
if dim == 2:
# Ensure 20A interlayer vacuum
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
# Remove all z k-points.
kpts_lines = open('KPOINTS').readlines()
with open('KPOINTS', 'w') as kpts:
for line in kpts_lines[:3]:
kpts.write(line)
kpts.write(kpts_lines[3].split()[0] + ' ' +
kpts_lines[3].split()[1] + ' 1')
# Submission script
if dim == 2:
binary = VASP_TWOD_BIN
elif dim == 3:
binary = VASP_STD_BIN
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
def get_hull_distance(competing_phase_directory='../competing_phases'):
"""
Calculate the material's distance to the thermodynamic hull,
based on species in the Materials Project database.
Args:
competing_phase_directory (str): absolute or relative path
to the location where your competing phases have been
relaxed. The default expectation is that they are stored
in a directory named 'competing_phases' at the same level
as your material's relaxation directory.
Returns:
float: distance (eV/atom) between the material and the
hull.
"""
finished_competitors = {}
original_directory = os.getcwd()
# Determine which competing phases have been relaxed in the current
# framework and store them in a dictionary ({formula: entry}).
if os.path.isdir(competing_phase_directory):
os.chdir(competing_phase_directory)
for comp_dir in [dir for dir in os.listdir(os.getcwd())
if os.path.isdir(dir) and is_converged(dir)]:
vasprun = Vasprun('{}/vasprun.xml'.format(comp_dir))
composition = vasprun.final_structure.composition
energy = vasprun.final_energy
finished_competitors[comp_dir] = ComputedEntry(composition, energy)
os.chdir(original_directory)
else:
raise ValueError('Competing phase directory does not exist.')
composition = Structure.from_file('POSCAR').composition
try:
energy = Vasprun('vasprun.xml').final_energy
except:
raise ValueError('This directory does not have a converged vasprun.xml')
my_entry = ComputedEntry(composition, energy) # 2D material
entries = MPR.get_entries_in_chemsys([elt.symbol for elt in composition])
# If the energies of competing phases have been calculated in
# the current framework, put them in the phase diagram instead
# of the MP energies.
for i in range(len(entries)):
formula = entries[i].composition.reduced_formula
if formula in finished_competitors:
entries[i] = finished_competitors[formula]
else:
entries[i] = ComputedEntry(entries[i].composition, 100)
entries.append(my_entry) # 2D material
#pda = PDAnalyzer(PhaseDiagram(entries))
pda = PhaseDiagram(entries)
decomp = pda.get_decomp_and_e_above_hull(my_entry, allow_negative=True)
return decomp[1]
def plot_ion_hull_and_voltages(ion, fmt='pdf'):
"""
Plots the phase diagram between the pure material and pure ion,
Connecting the points on the convex hull of the phase diagram.
Args:
ion (str): name of atom that was intercalated, e.g. 'Li'.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Calculated with the relax() function in
# mat2d.stability.startup. If you are using other input
# parameters, you need to recalculate these values!
ion_ev_fu = {'Li': -1.7540797, 'Mg': -1.31976062, 'Al': -3.19134607}
energy = Vasprun('vasprun.xml').final_energy
composition = Structure.from_file('POSCAR').composition
# Get the formula (with single-digit integers preceded by a '_').
twod_material = list(composition.reduced_formula)
twod_formula = str()
for i in range(len(twod_material)):
try:
int(twod_material[i])
twod_formula += '_{}'.format(twod_material[i])
except:
twod_formula += twod_material[i]
twod_ev_fu = energy / composition.get_reduced_composition_and_factor()[1]
data = [(0, 0, 0, twod_ev_fu)] # (at% ion, n_ions, E_F, abs_energy)
dirs = [dir for dir in os.listdir(os.getcwd()) if os.path.isdir(dir)]
for directory in dirs:
if is_converged(directory):
os.chdir(directory)
energy = Vasprun('vasprun.xml').final_energy
composition = Structure.from_file('POSCAR').composition
ion_fraction = composition.get_atomic_fraction(ion)
no_ion_comp_dict = composition.as_dict()
no_ion_comp_dict.update({ion: 0})
no_ion_comp = Composition.from_dict(no_ion_comp_dict)
n_twod_fu = no_ion_comp.get_reduced_composition_and_factor()[1]
n_ions = composition[ion] / n_twod_fu
E_F = ((energy - composition[ion] * ion_ev_fu[ion] -
twod_ev_fu * n_twod_fu)/ composition.num_atoms)
data.append((ion_fraction, n_ions, E_F, energy / n_twod_fu))
os.chdir('../')
data.append((1, 1, 0, ion_ev_fu[ion])) # Pure ion
sorted_data = sorted(data, key=operator.itemgetter(0))
# Determine which compositions are on the convex hull.
energy_profile = np.array([[item[0], item[2]] for item in sorted_data
if item[2] <= 0])
hull = ConvexHull(energy_profile)
convex_ion_fractions = [energy_profile[vertex, 0] for vertex in hull.vertices]
convex_formation_energies = [energy_profile[vertex, 1] for vertex in hull.vertices]
convex_ion_fractions.append(convex_ion_fractions.pop(0))
convex_formation_energies.append(convex_formation_energies.pop(0))
concave_ion_fractions = [pt[0] for pt in sorted_data
if pt[0] not in convex_ion_fractions]
concave_formation_energies = [pt[2] for pt in sorted_data
if pt[0] not in convex_ion_fractions]
voltage_profile = []
j = 0
k = 0
for i in range(1, len(sorted_data) - 1):
if sorted_data[i][0] in convex_ion_fractions:
voltage = -(((sorted_data[i][3] - sorted_data[k][3])-
(sorted_data[i][1] - sorted_data[k][1]) * ion_ev_fu[ion])
/ (sorted_data[i][1] - sorted_data[k][1]))
voltage_profile.append((sorted_data[k][0], voltage))
voltage_profile.append((sorted_data[i][0], voltage))
j += 1
k = i
voltage_profile.append((voltage_profile[-1][0], 0))
voltage_profile.append((1, 0))
voltage_profile_x = [tup[0] for tup in voltage_profile]
voltage_profile_y = [tup[1] for tup in voltage_profile]
ax = plt.figure(figsize=(14, 10)).gca()
ax.plot([0, 1], [0, 0], 'k--')
ax.plot(convex_ion_fractions, convex_formation_energies, 'b-', marker='o',
markersize=12, markeredgecolor='none')
ax.plot(concave_ion_fractions, concave_formation_energies, 'r', marker='o',
linewidth=0, markersize=12, markeredgecolor='none')
ax2 = ax.twinx()
ax2.plot(voltage_profile_x, voltage_profile_y, 'k-', marker='o')
ax.text(0, 0.002, r'$\mathrm{%s}$' % twod_formula, family='serif', size=24)
ax.text(0.99, 0.002, r'$\mathrm{%s}$' % ion, family='serif', size=24,
horizontalalignment='right')
ax.set_xticklabels(ax.get_xticks(), family='serif', size=20)
ax.set_yticklabels(ax.get_yticks(), family='serif', size=20)
ax2.set_yticklabels(ax2.get_yticks(), family='serif', size=20)
ax.set_xlabel('at% {}'.format(ion), family='serif', size=28)
ax.set_ylabel(r'$\mathrm{E_F\/(eV/atom)}$', size=28)
ax2.yaxis.set_label_position('right')
if ion == 'Li':
ax2.set_ylabel(r'$\mathrm{Potential\/vs.\/Li/Li^+\/(V)}$', size=28)
elif ion == 'Mg':
ax2.set_ylabel(r'$\mathrm{Potential\/vs.\/Mg/Mg^{2+}\/(V)}$', size=28)
elif ion == 'Al':
ax2.set_ylabel(r'$\mathrm{Potential\/vs.\/Al/Al^{3+}\/(V)}$', size=28)
plt.savefig('{}_hull.{}'.format(ion, fmt), transparent=True)
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 run_pbe_calculation(dim=2, submit=True, force_overwrite=False):
"""
Setup and submit a normal PBE calculation for band structure along
high symmetry k-paths.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
PBE_INCAR_DICT = {
'EDIFF': 1e-6,
'IBRION': 2,
'ISIF': 3,
'ISMEAR': 1,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 1,
'LREAL': 'Auto',
'NPAR': 4,
'PREC': 'Accurate',
'LWAVE': True,
'SIGMA': 0.1,
'ENCUT': 500,
'ISPIN': 2
}
directory = os.path.basename(os.getcwd())
if not os.path.isdir('pbe_bands'):
os.mkdir('pbe_bands')
if force_overwrite or not is_converged('pbe_bands'):
shutil.copy("CONTCAR", "pbe_bands/POSCAR")
if os.path.isfile('POTCAR'):
shutil.copy("POTCAR", "pbe_bands")
PBE_INCAR_DICT.update(
{'MAGMOM': get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(PBE_INCAR_DICT).write_file('pbe_bands/INCAR')
structure = Structure.from_file('POSCAR')
kpath = HighSymmKpath(structure)
Kpoints.automatic_linemode(20, kpath).write_file('pbe_bands/KPOINTS')
os.chdir('pbe_bands')
if dim == 2:
remove_z_kpoints()
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(directory, 16, '800mb', '6:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
def run_hse_calculation(dim=2,
submit=True,
force_overwrite=False,
destroy_prep_directory=False):
"""
Setup/submit an HSE06 calculation to get an accurate band structure.
Requires a previous IBZKPT from a standard DFT run. See
http://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure for more
details.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
destroy_prep_directory (bool): whether or not to remove
(rm -r) the hse_prep directory, if it exists. This
can help to automatically clean up and save space.
"""
HSE_INCAR_DICT = {
'LHFCALC': True,
'HFSCREEN': 0.2,
'AEXX': 0.25,
'ALGO': 'D',
'TIME': 0.4,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 11,
'LWAVE': True,
'NPAR': 8,
'PREC': 'Accurate',
'EDIFF': 1e-4,
'ENCUT': 450,
'ICHARG': 2,
'ISMEAR': 1,
'SIGMA': 0.1,
'IBRION': 2,
'ISIF': 3,
'ISPIN': 2
}
if not os.path.isdir('hse_bands'):
os.mkdir('hse_bands')
if force_overwrite or not is_converged('hse_bands'):
os.chdir('hse_bands')
os.system('cp ../CONTCAR ./POSCAR')
if os.path.isfile('../POTCAR'):
os.system('cp ../POTCAR .')
HSE_INCAR_DICT.update(
{'MAGMOM': get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(HSE_INCAR_DICT).write_file('INCAR')
# Re-use the irreducible brillouin zone KPOINTS from a
# previous standard DFT run.
if os.path.isdir('../hse_prep'):
ibz_lines = open('../hse_prep/IBZKPT').readlines()
if destroy_prep_directory:
os.system('rm -r ../hse_prep')
else:
ibz_lines = open('../IBZKPT').readlines()
n_ibz_kpts = int(ibz_lines[1].split()[0])
kpath = HighSymmKpath(Structure.from_file('POSCAR'))
Kpoints.automatic_linemode(20, kpath).write_file('KPOINTS')
if dim == 2:
remove_z_kpoints()
linemode_lines = open('KPOINTS').readlines()
abs_path = []
i = 4
while i < len(linemode_lines):
start_kpt = linemode_lines[i].split()
end_kpt = linemode_lines[i + 1].split()
increments = [(float(end_kpt[0]) - float(start_kpt[0])) / 20,
(float(end_kpt[1]) - float(start_kpt[1])) / 20,
(float(end_kpt[2]) - float(start_kpt[2])) / 20]
abs_path.append(start_kpt[:3] + ['0', start_kpt[4]])
for n in range(1, 20):
abs_path.append([
str(float(start_kpt[0]) + increments[0] * n),
str(float(start_kpt[1]) + increments[1] * n),
str(float(start_kpt[2]) + increments[2] * n), '0'
])
abs_path.append(end_kpt[:3] + ['0', end_kpt[4]])
i += 3
n_linemode_kpts = len(abs_path)
with open('KPOINTS', 'w') as kpts:
kpts.write('Automatically generated mesh\n')
kpts.write('{}\n'.format(n_ibz_kpts + n_linemode_kpts))
kpts.write('Reciprocal Lattice\n')
for line in ibz_lines[3:]:
kpts.write(line)
for point in abs_path:
kpts.write('{}\n'.format(' '.join(point)))
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob('{}_hsebands'.format(os.getcwd().split('/')[-2]),
2, 64, '1800mb', '50:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(
'{}_hsebands'.format(os.getcwd().split('/')[-2]), 64, '1800mb',
'50:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
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 run_hse_calculation(dim=2, submit=True, force_overwrite=False):
"""
Setup/submit an HSE06 calculation to get an accurate band structure.
See http://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure for
more details.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
HSE_INCAR_DICT = {
'LHFCALC': True,
'HFSCREEN': 0.2,
'AEXX': 0.25,
'ALGO': 'D',
'TIME': 0.4,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 11,
'LWAVE': True,
'NPAR': 8,
'PREC': 'Accurate',
'EDIFF': 1e-4,
'ENCUT': 450,
'ICHARG': 2,
'ISMEAR': 1,
'SIGMA': 0.1,
'IBRION': 2,
'ISIF': 3,
'ISPIN': 2
}
if not os.path.isdir('hse_bands'):
os.mkdir('hse_bands')
if force_overwrite or not is_converged('hse_bands'):
os.chdir('hse_bands')
os.system('cp ../CONTCAR ./POSCAR')
structure = Structure.from_file("POSCAR")
if os.path.isfile('../POTCAR'):
os.system('cp ../POTCAR .')
HSE_INCAR_DICT.update({'MAGMOM': get_magmom_string(structure)})
Incar.from_dict(HSE_INCAR_DICT).write_file('INCAR')
# Re-use the irreducible brillouin zone KPOINTS from a
# previous standard DFT run.
write_band_structure_kpoints(structure, dim=dim)
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob('{}_hsebands'.format(os.getcwd().split('/')[-2]),
2, 64, '1800mb', '50:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(
'{}_hsebands'.format(os.getcwd().split('/')[-2]), 64, '1800mb',
'50:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
