def plot_qpbands(self, bands_filepath, bands_label=None, dos_filepath=None, dos_args=None, **kwargs):
"""
Correct the energies found in the netcdf file bands_filepath and plot the band energies (both the initial
and the corrected ones) with matplotlib. The plot contains the KS and the QP DOS if dos_filepath is not None.
Args:
bands_filepath: Path to the netcdf file containing the initial KS energies to be corrected.
bands_label String used to label the KS bands in the plot.
dos_filepath: Optional path to a netcdf file with the initial KS energies on a homogeneous k-mesh
(used to compute the KS and the QP dos)
dos_args: Dictionary with the arguments passed to get_dos to compute the DOS
Used if dos_filepath is not None.
kwargs: Options passed to the plotter.
Returns:
matplotlib figure
"""
from abipy.abilab import abiopen, ElectronBandsPlotter
# Read the KS band energies from bands_filepath and apply the scissors operator.
with abiopen(bands_filepath) as ncfile: ks_bands = ncfile.ebands
qp_bands = ks_bands.apply_scissors(self._scissors_spin)
# Read the band energies computed on the Monkhorst-Pack (MP) mesh and compute the DOS.
ks_dos, qp_dos = None, None
if dos_filepath is not None:
with abiopen(dos_filepath) as ncfile: ks_mpbands = ncfile.ebands
dos_args = {} if not dos_args else dos_args
ks_dos = ks_mpbands.get_edos(**dos_args)
# Compute the DOS with the modified QPState energies.
qp_mpbands = ks_mpbands.apply_scissors(self._scissors_spin)
qp_dos = qp_mpbands.get_edos(**dos_args)
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
bands_label = bands_label if bands_label is not None else os.path.basename(bands_filepath)
plotter.add_ebands(bands_label, ks_bands, dos=ks_dos)
plotter.add_ebands(bands_label + " + scissors", qp_bands, dos=qp_dos)
return plotter.plot(**kwargs)
# Read the KS band energies computed on the Monkhorst-Pack (MP) mesh
# and compute the DOS with the Gaussian method
ks_mpbands = abiopen(abidata.ref_file("si_scf_GSR.nc")).ebands
ks_dos = ks_mpbands.get_edos()
# Apply the scissors operator first on the KS band structure
# along the k-path then on the energies computed with the MP mesh.
qp_bands = ks_bands.apply_scissors(scissors)
qp_mpbands = ks_mpbands.apply_scissors(scissors)
# Compute the DOS with the modified QPState energies.
qp_dos = qp_mpbands.get_edos()
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_bands, dos=ks_dos)
plotter.add_ebands("LDA+scissors(e)", qp_bands, dos=qp_dos)
# Define the mapping reduced_coordinates -> name of the k-point.
klabels = {
(0.5, 0.0, 0.0): "L",
(0.0, 0.0, 0.0): "$\Gamma$",
(0.0, 0.5, 0.5): "X",
}
plotter.plot(title="Silicon band structure", klabels=klabels)
ks_mpbands = abiopen(abidata.ref_file("si_scf_GSR.nc")).ebands
ks_dos = ks_mpbands.get_edos()
# Apply the scissors operator first on the KS band structure
# along the k-path then on the energies computed with the MP mesh.
qp_bands = ks_bands.apply_scissors(scissors)
qp_mpbands = ks_mpbands.apply_scissors(scissors)
# Compute the DOS with the modified QPState energies.
qp_dos = qp_mpbands.get_edos()
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_bands, dos=ks_dos)
plotter.add_ebands("LDA+scissors(e)", qp_bands, dos=qp_dos)
# Define the mapping reduced_coordinates -> name of the k-point.
klabels = {
(0.5, 0.0, 0.0): "L",
(0.0, 0.0, 0.0): "$\Gamma$",
(0.0, 0.5, 0.5): "X",
}
plotter.plot(title="Silicon band structure", klabels=klabels)
except (IOError, OSError):
print('no abinit output found')
def plot_qpbands(self,
bands_filepath,
bands_label=None,
dos_filepath=None,
dos_args=None,
qp_marker=None,
**kwargs):
"""
Correct the energies found in the netcdf file bands_filepath and plot the band energies (both the initial
and the corrected ones) with matplotlib. The plot contains the KS and the QP DOS if dos_filepath is not None.
Args:
bands_filepath: Path to the netcdf file containing the initial KS energies to be corrected.
bands_label String used to label the KS bands in the plot.
dos_filepath: Optional path to a netcdf file with the initial KS energies on a homogeneous k-mesh
(used to compute the KS and the QP dos)
dos_args: Dictionary with the arguments passed to get_dos to compute the DOS
Used if dos_filepath is not None.
qp_marker: if int > 0, markers for the ab-initio QP energies are displayed. e.g qp_marker=50
kwargs: Options passed to the plotter.
Returns:
matplotlib figure
"""
from abipy.abilab import abiopen, ElectronBandsPlotter
# Read the KS band energies from bands_filepath and apply the scissors operator.
with abiopen(bands_filepath) as ncfile:
ks_bands = ncfile.ebands
#structure = ncfile.structure
qp_bands = ks_bands.apply_scissors(self._scissors_spin)
# Read the band energies computed on the Monkhorst-Pack (MP) mesh and compute the DOS.
ks_dos, qp_dos = None, None
if dos_filepath is not None:
with abiopen(dos_filepath) as ncfile:
ks_mpbands = ncfile.ebands
dos_args = {} if not dos_args else dos_args
ks_dos = ks_mpbands.get_edos(**dos_args)
# Compute the DOS with the modified QPState energies.
qp_mpbands = ks_mpbands.apply_scissors(self._scissors_spin)
qp_dos = qp_mpbands.get_edos(**dos_args)
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
bands_label = bands_label if bands_label is not None else os.path.basename(
bands_filepath)
plotter.add_ebands(bands_label, ks_bands, dos=ks_dos)
plotter.add_ebands(bands_label + " + scissors", qp_bands, dos=qp_dos)
#qp_marker = 50
if qp_marker is not None:
# Compute correspondence between the k-points in qp_list and the k-path in qp_bands.
# TODO
# WARNING: strictly speaking one should check if qp_kpoint is in the star of k-point.
# but compute_star is too slow if written in pure python.
x, y, s = [], [], []
for ik_path, kpoint in enumerate(qp_bands.kpoints):
#kstar = kpoint.compute_star(structure.fm_symmops)
for spin in range(self.nsppol):
for ik_qp, qp in enumerate(self._qps_spin[spin]):
if qp.kpoint == kpoint:
#if qp.kpoint in kstar:
x.append(ik_path)
y.append(np.real(qp.qpe))
s.append(qp_marker)
plotter.set_marker("ab-initio QP", [x, y, s])
return plotter.plot(**kwargs)
def band_plots(self, query=None, sort='system'):
"""
Plot the scissored bands for all the systems in the DB
:param query:
:param sort:
:return:
"""
if query is None:
query = {}
for item in self.col.find(query).sort(sort):
exclude = ['ZnO_mp-2133', 'K3Sb_mp-14017', 'NiP2_mp-486', 'OsS2_mp-20905', 'PbO_mp-1336', 'Rb3Sb_mp-16319',
'As2Os_mp-2455']
if item['system'] in exclude:
continue
if False:
print('System : ', item['system'].split('_mp-')[0])
print('Ps : ', item['ps'])
print('extra : ', item['extra_vars'])
print('gwresults : ', item['gw_results'])
try:
data = self.gfs.get(item['results_file']).read()
if len(data) > 1000:
srf = MySigResFile(data)
title = "QPState corrections of " + str(item['system']) + "\nusing " \
+ str(item['ps'].split('/')[-2])
if item['extra_vars'] is not None:
title += ' and ' + str(self.fix_extra(item['extra_vars']))
srf.plot_scissor(title=title)
srf.print_gap_info()
sc = srf.get_scissor()
with self.gfs.get(item['ksbands_file']) as f:
ksb = MyBandsFile(f.read()).ebands
qpb = ksb.apply_scissors(sc)
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("KS", ksb)
plotter.add_ebands("KS+scissors(e)", qpb)
fig = plotter.plot(align='cbm', ylim=(-5, 10), title="%s Bandstructure" %
item['system'].split('_mp-')[0])
try:
if not item['tgwgap']:
bands_data = self.gfs.get(item['ksbands_file'])
ks_bands = MyBandsFile(bands_data)
item['tkshomo'] = ks_bands.h**o
item['tkslumo'] = ks_bands.lumo
item['tksgap'] = ks_bands.lumo - ks_bands.h**o
item['tgwhomo'] = ks_bands.h**o + sc.apply(ks_bands.h**o)
item['tgwlumo'] = ks_bands.lumo + sc.apply(ks_bands.lumo)
item['tgwgap'] = item['tgwlumo'] - item['tgwhomo']
self.col.save(item)
except KeyError:
pass
except (KeyError, IOError, NoFile):
print('No Sigres file in DataBase')
try:
return fig
except UnboundLocalError:
return None
def plot_qpbands(self, bands_filepath, bands_label=None, dos_filepath=None, dos_args=None, qp_marker=None, **kwargs):
"""
Correct the energies found in the netcdf file bands_filepath and plot the band energies (both the initial
and the corrected ones) with matplotlib. The plot contains the KS and the QP DOS if dos_filepath is not None.
Args:
bands_filepath: Path to the netcdf file containing the initial KS energies to be corrected.
bands_label String used to label the KS bands in the plot.
dos_filepath: Optional path to a netcdf file with the initial KS energies on a homogeneous k-mesh
(used to compute the KS and the QP dos)
dos_args: Dictionary with the arguments passed to get_dos to compute the DOS
Used if dos_filepath is not None.
qp_marker: if int > 0, markers for the ab-initio QP energies are displayed. e.g qp_marker=50
kwargs: Options passed to the plotter.
Returns:
matplotlib figure
"""
from abipy.abilab import abiopen, ElectronBandsPlotter
# Read the KS band energies from bands_filepath and apply the scissors operator.
with abiopen(bands_filepath) as ncfile:
ks_bands = ncfile.ebands
#structure = ncfile.structure
qp_bands = ks_bands.apply_scissors(self._scissors_spin)
# Read the band energies computed on the Monkhorst-Pack (MP) mesh and compute the DOS.
ks_dos, qp_dos = None, None
if dos_filepath is not None:
with abiopen(dos_filepath) as ncfile: ks_mpbands = ncfile.ebands
dos_args = {} if not dos_args else dos_args
ks_dos = ks_mpbands.get_edos(**dos_args)
# Compute the DOS with the modified QPState energies.
qp_mpbands = ks_mpbands.apply_scissors(self._scissors_spin)
qp_dos = qp_mpbands.get_edos(**dos_args)
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
bands_label = bands_label if bands_label is not None else os.path.basename(bands_filepath)
plotter.add_ebands(bands_label, ks_bands, dos=ks_dos)
plotter.add_ebands(bands_label + " + scissors", qp_bands, dos=qp_dos)
#qp_marker = 50
if qp_marker is not None:
# Compute correspondence between the k-points in qp_list and the k-path in qp_bands.
# TODO
# WARNING: strictly speaking one should check if qp_kpoint is in the star of k-point.
# but compute_star is too slow if written in pure python.
x, y, s = [], [], []
for ik_path, kpoint in enumerate(qp_bands.kpoints):
#kstar = kpoint.compute_star(structure.fm_symmops)
for spin in range(self.nsppol):
for ik_qp, qp in enumerate(self._qps_spin[spin]):
if qp.kpoint == kpoint:
#if qp.kpoint in kstar:
x.append(ik_path)
y.append(np.real(qp.qpe))
s.append(qp_marker)
plotter.set_marker("ab-initio QP", [x, y, s])
return plotter.plot(**kwargs)
# Read the KS band energies computed on the Monkhorst-Pack (MP) mesh
# and compute the DOS with the Gaussian method
ks_mpbands = abiopen(abidata.ref_file("si_scf_GSR.nc")).ebands
ks_dos = ks_mpbands.get_edos()
# Apply the scissors operator first on the KS band structure
# along the k-path then on the energies computed with the MP mesh.
qp_bands = ks_bands.apply_scissors(scissors)
qp_mpbands = ks_mpbands.apply_scissors(scissors)
# Compute the DOS with the modified QPState energies.
qp_dos = qp_mpbands.get_edos()
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_bands, dos=ks_dos)
plotter.add_ebands("LDA+scissors(e)", qp_bands, dos=qp_dos)
# Define the mapping reduced_coordinates -> name of the k-point.
klabels = {
(0.5, 0.0, 0.0): "L",
(0.0, 0.0, 0.0): "$\Gamma$",
(0.0, 0.5, 0.5): "X",
}
plotter.plot(title="Silicon band structure", klabels=klabels, align='cbm')
