def showElectronDosFrame(parent, filepath):
"""
Read the electron bands from file filepath and shows an `ElectronDosFrame`.
"""
bands = ElectronBands.from_file(filepath)
title = "File: %s" % os.path.relpath(filepath)
ElectronDosFrame(parent, bands, title=title).Show()
def test_jdos(self):
"""Test JDOS methods."""
bands = ElectronBands.from_file(get_reference_file("si_WFK-etsf.nc"))
spin = 0
conduction = [4,]
for v in range(1,5):
valence = range(0,v)
jdos = bands.get_jdos(spin, valence, conduction)
intg = jdos.integral()[-1][-1]
self.assert_almost_equal(intg, len(conduction) * len(valence))
# Need a homogeneous sampling.
with self.assertRaises(ValueError):
bands = ElectronBands.from_file(get_reference_file("si_nscf_WFK-etsf.nc"))
bands.get_jdos(spin, 0, 4)
def showElectronDosFrame(parent, filepath):
"""
Read the electron bands from file filepath and shows an `ElectronDosFrame`.
"""
bands = ElectronBands.from_file(filepath)
title = "File: %s" % os.path.relpath(filepath)
ElectronDosFrame(parent, bands, title=title).Show()
def showElectronBandsPlot(parent, filepath):
"""
Read the electron bands from file filepath and plot the bands.
"""
ebands = ElectronBands.from_file(filepath)
title = "File: %s" % os.path.relpath(filepath)
ebands.plot(title=title)
def model_from_ebands(cls, ebands, tmesh=(0, 300, 600), poorman_polaron=False):
ebands = ElectronBands.as_ebands(ebands)
ntemp = len(tmesh)
nwr = 1000
wr_step = 0.01
aw = np.empty((ebands.nsppol, ebands.nkpt, ebands.mband, ntemp, nwr))
aw_meshes = np.empty((ebands.nsppol, ebands.nkpt, ebands.mband, nwr))
#aw: [nwr, ntemp, max_nbcalc, nkcalc, nsppol] array
#aw_meshes: [max_nbcalc, nkcalc, nsppol] array with energy mesh in eV
from abipy.tools.numtools import lorentzian
from scipy.integrate import cumtrapz
for spin in ebands.spins:
for ik, kpt in enumerate(ebands.kpoints):
for band in range(ebands.nband_sk[spin, ik]):
e0 = ebands.eigens[spin, ik, band]
emin = e0 - wr_step * (nwr // 2)
emax = e0 + wr_step * (nwr // 2)
emesh = np.linspace(emin, emax, num=nwr)
aw_meshes[spin, ik, band] = emesh
# Naive model: lorentzian centered on KS energy with T-dep broadening
for itemp, temp in enumerate(tmesh):
width = 0.2 + (temp / 300) * 0.2
avals = lorentzian(emesh, width=width, center=e0, height=None)
if poorman_polaron:
if band in (1, 2, 3) and kpt.norm < 0.3:
avals += 1.1 * lorentzian(emesh, width=0.1 * width, center=e0 - 0.4, height=None)
avals /= cumtrapz(avals, x=emesh)[-1]
aw[spin, ik, band, itemp] = avals
return cls(ebands, aw, aw_meshes, tmesh)
def model_from_ebands(cls, ebands, tmesh=(0, 300, 600), poorman_polaron=False):
ebands = ElectronBands.as_ebands(ebands)
ntemp = len(tmesh)
nwr = 1000
wr_step = 0.01
aw = np.empty((ebands.nsppol, ebands.nkpt, ebands.mband, ntemp, nwr))
aw_meshes = np.empty((ebands.nsppol, ebands.nkpt, ebands.mband, nwr))
#aw: [nwr, ntemp, max_nbcalc, nkcalc, nsppol] array
#aw_meshes: [max_nbcalc, nkcalc, nsppol] array with energy mesh in eV
from abipy.tools.numtools import lorentzian
from scipy.integrate import cumtrapz
for spin in ebands.spins:
for ik, kpt in enumerate(ebands.kpoints):
for band in range(ebands.nband_sk[spin, ik]):
e0 = ebands.eigens[spin, ik, band]
emin = e0 - wr_step * (nwr // 2)
emax = e0 + wr_step * (nwr // 2)
emesh = np.linspace(emin, emax, num=nwr)
aw_meshes[spin, ik, band] = emesh
# Naive model: lorentzian centered on KS energy with T-dep broadening
for itemp, temp in enumerate(tmesh):
width = 0.2 + (temp / 300) * 0.2
avals = lorentzian(emesh, width=width, center=e0, height=None)
if poorman_polaron:
if band in (1, 2, 3) and kpt.norm < 0.3:
avals += 1.1 * lorentzian(emesh, width=0.1 * width, center=e0 - 0.4, height=None)
avals /= cumtrapz(avals, x=emesh)[-1]
aw[spin, ik, band, itemp] = avals
return cls(ebands, aw, aw_meshes, tmesh)
def showElectronBandsPlot(parent, filepath):
"""
Read the electron bands from file filepath and plot the bands.
"""
ebands = ElectronBands.from_file(filepath)
title = "File: %s" % os.path.relpath(filepath)
ebands.plot(title=title)
def __init__(self, filepath):
"""
Initialized the object from a Netcdf file.
"""
super(WFK_File, self).__init__(filepath)
# Initialize the structure from file.
self.structure = Structure.from_file(filepath)
# Initialize the band energies.
self.bands = ElectronBands.from_file(filepath)
self.kpoints = kpoints_factory(filepath)
self.nkpt = len(self.kpoints)
with WFK_Reader(filepath) as reader:
assert reader.has_pwbasis_set
assert reader.cplex_ug == 2
self.npwarr = reader.npwarr
self.nband_sk = reader.nband_sk
self.nspinor = reader.nspinor
self.nsppol = reader.nsppol
self.nspden = reader.nspden
# FFT mesh (augmented divisions reported in the WFK file)
self.fft_mesh = Mesh3D(reader.fft_divs, self.structure.lattice_vectors())
# Build G-spheres for each k-point
gspheres = len(self.kpoints) * [None]
ecut = reader.ecut
for k, kpoint in enumerate(self.kpoints):
gvec_k, istwfk = reader.read_gvec_istwfk(k)
gspheres[k] = GSphere(ecut, self.structure.reciprocal_lattice, kpoint, gvec_k, istwfk=istwfk)
self._gspheres = tuple(gspheres)
# Save reference to the reader.
self.reader = reader
def test_dos(self):
"""Test DOS methods."""
gs_bands = ElectronBands.from_file(get_reference_file("si_WFK-etsf.nc"))
dos = gs_bands.get_dos()
mu = dos.find_mu(8, atol=1.e-4)
self.assert_almost_equal(mu, 6.1443350264585996, decimal=4)
def test_ncread_ebands(self):
"""Read ElectronBands from WFK data files"""
for filename in WFK_NCFILES:
bands = ElectronBands.from_file(filename)
def read_bands(self, path):
try:
self.bands = ElectronBands.from_file(path)
ewx.ElectronDosFrame(bands=self.bands, parent=self).Show()
except Exception:
awx.showErrorMessage(self)
def showElectronJdosFrame(parent, filepath):
bands = ElectronBands.from_file(filepath)
ElectronJdosFrame(parent, bands).Show()
def showElectronDosFrame(parent, filepath):
bands = ElectronBands.from_file(filepath)
title = "File: %s" % os.path.relpath(filepath)
ElectronDosFrame(parent, bands, title=title).Show()
def showElectronJdosFrame(parent, filepath):
"""
Read the electron bands from file filepath and shows an `ElectronJdosFrame`.
"""
ebands = ElectronBands.from_file(filepath)
ElectronJdosFrame(parent, ebands).Show()
def showElectronBandsPlot(parent, filepath):
ebands = ElectronBands.from_file(filepath)
title = "File: %s" % os.path.relpath(filepath)
ebands.plot(title=title)
def showElectronJdosFrame(parent, filepath):
"""
Read the electron bands from file filepath and shows an `ElectronJdosFrame`.
"""
ebands = ElectronBands.from_file(filepath)
ElectronJdosFrame(parent, ebands).Show()
def showElectronDosFrame(parent, filepath):
bands = ElectronBands.from_file(filepath)
ElectronDosFrame(parent, bands, title="File: %s" % filepath).Show()
def showElectronBandsPlot(parent, filepath):
bands = ElectronBands.from_file(filepath)
bands.plot(title="File: %s" % filepath)
def build_scissors(options, args):
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
#gw_fname = raw_input('Enter the name of the GW file: ').strip()
#
# Init the corrections from gw_fname
try:
gw_fname = options.gw_files[0]
except:
show_examples_and_exit(1, err_msg = "GW file name must be specified")
qp_corrections = read_GWFile(gw_fname)
#
# Construct the scissors operator for each spin.
nsppol = len(qp_corrections)
scissor_spin = list()
for spin in range(nsppol):
qpc = qp_corrections[spin].sort_by_energy()
e0mesh = qpc.get_e0mesh()
e0_min = np.min(e0mesh)
e0_max = np.max(e0mesh)
#print e0_min, e0_max
corr = qpc.get_qpcorr()
vb_idx = raw_input('Enter the index of the valence band maximum: ')
vb_idx = int(vb_idx)
h**o = qpc.max_e0(vb_idx)
lumo = qpc.min_e0(vb_idx + 1)
#print h**o, lumo
#qpc.plot()
ndomains = raw_input('How many fitting intervals do you want? (default is 2: valence/conduction): ')
if ndomains:
ndomains = int(ndomains)
s = raw_input('Enter the boundaries for domains: ')
tokens = s.split(",")
domains = list()
for t in tokens:
bound = [float(v) for v in t.split()]
domains.append(bound)
print("Domains are: ", bound)
else:
ndomains = 2
pad_hl = 0.1 / Ha_eV
#h**o += 0.00000001
#lumo -= 0.00000001
domains = [(e0_min - pad_hl, h**o), (lumo, e0_max + pad_hl)]
sciss = qpc.make_scissor(domains)
qpc.plot(scissor=sciss)
scissor_spin.append(sciss)
#return scissor_spin
# Save the list of objects with cPickle.
# fname = "SCISSOR.cpickle"
# fh = file(fname, mode="wb")
# pickle.dump(scissor_spin, fh)
# fh.close()
#bst_fname = raw_input('Enter the name of the band structure file: ').strip()
bst_fname = options.bands_file
ks_bands = ElectronBands.from_file(bst_fname)
qp_bands = ks_bands.apply_scissors(scissor_spin)
# Plot the KS and the QPState band structures.
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.grid(True)
#ax.legend(loc="upper left")
#title = None
#if title: ax.set_title(title)
ax.set_xlabel('k-point')
ax.set_ylabel('Energy [eV]')
for spin in range(ks_bands.nsppol):
for band in range(ks_bands.mband):
ks_bands.plot_ax(ax, spin, band)
qp_bands.plot_ax(ax, spin, band)
plt.show()
#qp_bands.raw_print(fh=None, units="eV")
# Write the GW file with the updated band structure.
gw_fname = raw_input('Enter the name of the GW file: ').strip()
if gw_fname: qp_bands.write_GWfile(gw_fname, ks_bands)
