def _find_iqpt_qpoint(self, qpoint):
if duck.is_intlike(qpoint):
iq = qpoint
qpoint = self.qpoints[iq]
else:
qpoint = Kpoint.as_kpoint(qpoint, self.structure.reciprocal_lattice)
iq = self.qpoints.index(qpoint)
return iq, qpoint
def __init__(self, qpoint, freq, displ_cart, structure):
"""
Args:
qpoint: qpoint in reduced coordinates.
freq: Phonon frequency in eV.
displ: Displacement (Cartesian coordinates, Angstrom)
structure: :class:`Structure` object.
"""
self.qpoint = Kpoint.as_kpoint(qpoint, structure.reciprocal_lattice)
self.freq = freq
self.displ_cart = displ_cart
self.structure = structure
def __init__(self, qpoint, freq, displ_cart, structure):
"""
Args:
qpoint: qpoint in reduced coordinates.
freq: Phonon frequency in eV.
displ: Displacement (Cartesian coordinates, Angstrom)
structure: :class:`Structure` object.
"""
self.qpoint = Kpoint.as_kpoint(qpoint, structure.reciprocal_lattice)
self.freq = freq
self.displ_cart = displ_cart
self.structure = structure
def plot_gkq2_qpath(self, band_kq, band_k, kpoint=0, with_glr=False, qdamp=None, nu_list=None, # spherical_average=False,
ax=None, fontsize=8, eph_wtol=EPH_WTOL, **kwargs):
r"""
Plot the magnitude of the electron-phonon matrix elements <k+q, band_kq| Delta_{q\nu} V |k, band_k>
for a given set of (band_kq, band, k) as a function of the q-point.
Args:
band_ks: Band index of the k+q states (starts at 0)
band_k: Band index of the k state (starts at 0)
kpoint: |Kpoint| object or index.
with_glr: True to plot the long-range component estimated from Verdi's model.
qdamp:
nu_list: List of phonons modes to be selected (starts at 0). None to select all modes.
ax: |matplotlib-Axes| or None if a new figure should be created.
fontsize: Label and title fontsize.
Return: |matplotlib-Figure|
"""
if duck.is_intlike(kpoint):
ik = kpoint
kpoint = self.kpoints[ik]
else:
kpoint = Kpoint.as_kpoint(kpoint, self.abifiles[0].structure.reciprocal_lattice)
ik = self.kpoints.index(kpoint)
# Assume abifiles are already ordered according to q-path.
xs = list(range(len(self.abifiles)))
natom3 = len(self.abifiles[0].structure) * 3
nsppol = self.abifiles[0].nsppol
nqpt = len(self.abifiles)
gkq_snuq = np.empty((nsppol, natom3, nqpt), dtype=np.complex)
if with_glr: gkq_lr = np.empty((nsppol, natom3, nqpt), dtype=np.complex)
# TODO: Should take into account possible degeneracies in k and kq...
xticks, xlabels = [], []
for iq, abifile in enumerate(self.abifiles):
qpoint = abifile.qpoint
#d3q_fact = one if not spherical_average else np.sqrt(4 * np.pi) * qpoint.norm
name = qpoint.name if qpoint.name is not None else abifile.structure.findname_in_hsym_stars(qpoint)
if qpoint.name is not None:
xticks.append(iq)
xlabels.append(name)
phfreqs_ha, phdispl_red = abifile.phfreqs_ha, abifile.phdispl_red
ncvar = abifile.reader.read_variable("gkq")
for spin in range(nsppol):
gkq_atm = ncvar[spin, ik, :, band_k, band_kq]
gkq_atm = gkq_atm[:, 0] + 1j * gkq_atm[:, 1]
# Transform the gkk matrix elements from (atom, red_direction) basis to phonon-mode basis.
gkq_snuq[spin, :, iq] = 0.0
for nu in range(natom3):
if phfreqs_ha[nu] < eph_wtol: continue
gkq_snuq[spin, nu, iq] = np.dot(phdispl_red[nu], gkq_atm) / np.sqrt(2.0 * phfreqs_ha[nu])
if with_glr:
# Compute long range part with (simplified) generalized Frohlich model.
gkq_lr[spin, :, iq] = glr_frohlich(qpoint, abifile.becs_cart, abifile.epsinf_cart,
abifile.phdispl_cart_bohr, phfreqs_ha, abifile.structure, qdamp=qdamp)
ax, fig, plt = get_ax_fig_plt(ax=ax)
nu_list = list(range(natom3)) if nu_list is None else list(nu_list)
for spin in range(nsppol):
for nu in nu_list:
ys = np.abs(gkq_snuq[spin, nu]) * abu.Ha_meV
pre_label = kwargs.pop("pre_label",r"$g_{\bf q}$")
if nsppol == 1: label = r"%s $\nu$: %s" % (pre_label, nu)
if nsppol == 2: label = r"%s $\nu$: %s, spin: %s" % (pre_label, nu, spin)
ax.plot(xs, ys, linestyle="--", label=label)
if with_glr:
# Plot model with G = 0 and delta_nn'
ys = np.abs(gkq_lr[spin, nu]) * abu.Ha_meV
label = r"$g_{\bf q}^{\mathrm{lr0}}$ $\nu$: %s" % nu
ax.plot(xs, ys, linestyle="", marker="o", label=label)
ax.grid(True)
ax.set_xlabel("Wave Vector")
ax.set_ylabel(r"$|g_{\bf q}|$ (meV)")
if xticks:
ax.set_xticks(xticks, minor=False)
ax.set_xticklabels(xlabels, fontdict=None, minor=False, size=kwargs.pop("klabel_size", "large"))
ax.legend(loc="best", fontsize=fontsize, shadow=True)
title = r"$band_{{\bf k} + {\bf q}: %s, band_{\bf{k}}: %s, kpoint: %s" % (band_kq, band_k, repr(kpoint))
ax.set_title(title, fontsize=fontsize)
return fig
