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Finalize max_phfreq option

This commit is contained in:
Matteo Giantomassi 2018-07-25 09:44:20 +02:00
parent 205c69adbe
commit defecb836b
1 changed files with 73 additions and 65 deletions
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138
abipy/electrons/ebands.py
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@ -168,13 +168,20 @@ class ElectronTransition(object):
"""
This object describes an electronic transition between two single-particle states.
"""
def __init__(self, in_state, out_state):
def __init__(self, in_state, out_state, all_kinds=None):
"""
Args:
in_state, out_state: Initial and finale state (:class:`Electron` instances).
all_kinds: List of tuple. Each tuple gives the index of the k-point of the (initial, final) state.
Used to plot e.g. all the optical gaps when there are equivalent k-points along the path.
"""
self.in_state = in_state
self.out_state = out_state
if all_kinds is None:
self.all_kinds = [(self.in_state.kidx, self.out_state.kidx)]
else:
# Provide default.
self.all_kinds = all_kinds
def __str__(self):
return self.to_string()
@ -1137,12 +1144,10 @@ class ElectronBands(Has_Structure):
Build an instance of :class:`Electron` from the spin, kpoint and band index
"""
kidx = self.kindex(kpoint)
#print("kidx", kidx)
eig = self.eigens[spin, kidx, band]
return Electron(spin=spin,
kpoint=self.kpoints[kidx],
band=band,
eig=eig,
eig=self.eigens[spin, kidx, band],
occ=self.occfacts[spin, kidx, band],
kidx=kidx,
#fermie=self.fermie
@ -1209,9 +1214,6 @@ class ElectronBands(Has_Structure):
blist.append(b)
enes.append(self.eigens[spin,k,b])
#enes = np.array(enes)
#kinds = np.where(enes == enes.max())[0]
#homo_kidx = kinds[len(kinds) // 2]
homo_kidx = np.array(enes).argmax()
homo_band = blist[homo_kidx]
@ -1273,7 +1275,7 @@ class ElectronBands(Has_Structure):
@lazy_property
def direct_gaps(self):
"""List of :class:`ElectronTransition` with info on the direct gaps for each spin."""
"""List of `nsppol` :class:`ElectronTransition` with info on the direct gaps for each spin."""
dirgaps = self.nsppol * [None]
for spin in self.spins:
gaps = []
@ -1286,11 +1288,13 @@ class ElectronBands(Has_Structure):
# If there multiple k-points along the path, prefer the one in the center
# If not possible e.g. direct at G with G-X-L-G path avoid points on
# the right border of the graph
#gaps = np.array(gaps)
#kinds = np.where(gaps == gaps.min())[0]
gaps = np.array(gaps)
kinds = np.where(gaps == gaps.min())[0]
kdir = kinds[0]
all_kinds = list(zip(kinds, kinds))
#kdir = kinds[len(kinds) // 2]
kdir = np.array(gaps).argmin()
dirgaps[spin] = ElectronTransition(self.homo_sk(spin, kdir), self.lumo_sk(spin, kdir))
#kdir = np.array(gaps).argmin()
dirgaps[spin] = ElectronTransition(self.homo_sk(spin, kdir), self.lumo_sk(spin, kdir), all_kinds=all_kinds)
return dirgaps
@ -1777,12 +1781,12 @@ class ElectronBands(Has_Structure):
or scalar e.g. ``left``. If left (right) is None, default values are used
points: Marker object with the position and the size of the marker.
Used for plotting purpose e.g. QP energies, energy derivatives...
with_gaps: True to add marker and arrows showing the fundamental and the direct gap.
max_phfreq: Max phonon frequency in eV to activate the scatterplot showing
the phonon absorptions/emission processes. All final states whose energy
is within +- max_phfreq of the initial state are included.
By default, the four electronic states defining the fundamental and the direct gap
are treated as initial state (not available for metals).
with_gaps: True to add markers and arrows showing the fundamental and the direct gap.
max_phfreq: Max phonon frequency in eV to activate scatterplot showing
possible phonon absorption/emission processes based on energy-conservation alone.
All final states whose energy is within +- max_phfreq of the initial state are included.
By default, the four electronic states defining the fundamental and the direct gaps
are considered as initial state (not available for metals).
fontsize: fontsize for legends and titles
Returns: |matplotlib-Figure|
@ -1809,10 +1813,8 @@ class ElectronBands(Has_Structure):
# Plot the band energies.
for spin in spin_list:
if spin == 0:
opts = {"color": "black", "linewidth": 2.0}
else:
opts = {"color": "red", "linewidth": 2.0}
opts = {"color": "black", "linewidth": 2.0} if spin == 0 else \
{"color": "red", "linewidth": 2.0}
# This to pass kwargs to plot_ax and avoid both lw and linewidth in opts
if "lw" in kwargs: opts.pop("linewidth")
opts.update(kwargs)
@ -1836,46 +1838,46 @@ class ElectronBands(Has_Structure):
arrow_opts.update(lw=2, alpha=0.6, arrowstyle="->", connectionstyle='arc3',
mutation_scale=20, zorder=1000)
scatter_opts = {"color": "blue"} if spin == 0 else {"color": "green"}
scatter_opts.update(marker="o", alpha=1.0, s=80, zorder=100)
scatter_opts.update(marker="o", alpha=1.0, s=80, zorder=100, edgecolor='black')
# Fundamental gap.
posA = (f_gap.in_state.kidx, f_gap.in_state.eig - e0)
posB = (f_gap.out_state.kidx, f_gap.out_state.eig - e0)
ax.scatter(posA[0], posA[1], **scatter_opts)
ax.scatter(posB[0], posB[1], **scatter_opts)
if need_arrows:
ax.add_patch(FancyArrowPatch(posA=posA, posB=posB, **arrow_opts))
if d_gap != f_gap:
# Direct gap.
posA = (d_gap.in_state.kidx, d_gap.in_state.eig - e0)
posB = (d_gap.out_state.kidx, d_gap.out_state.eig - e0)
for ik1, ik2 in f_gap.all_kinds:
posA = (ik1, f_gap.in_state.eig - e0)
posB = (ik2, f_gap.out_state.eig - e0)
ax.scatter(posA[0], posA[1], **scatter_opts)
ax.scatter(posB[0], posB[1], **scatter_opts)
if need_arrows:
ax.add_patch(FancyArrowPatch(posA=posA, posB=posB, **arrow_opts))
if d_gap != f_gap:
# Direct gap.
for ik1, ik2 in d_gap.all_kinds:
posA = (ik1, d_gap.in_state.eig - e0)
posB = (ik2, d_gap.out_state.eig - e0)
ax.scatter(posA[0], posA[1], **scatter_opts)
ax.scatter(posB[0], posB[1], **scatter_opts)
if need_arrows:
ax.add_patch(FancyArrowPatch(posA=posA, posB=posB, **arrow_opts))
gaps_string = self.get_gaps_string()
if gaps_string:
ax.set_title(gaps_string, fontsize=fontsize)
if max_phfreq is not None and (self.mband > self.nspinor * self.nelect // 2):
#f_gap = self.fundamental_gaps[spin]
#d_gap = self.direct_gaps[spin]
#if d_gap != f_gap:
# Add markers showing phonon absorption/emission processes.
for spin in self.spins:
scatter_opts = {"color": "steelblue"} if spin == 0 else {"color": "teal"}
scatter_opts.update(alpha=0.6, s=40, zorder=10)
#scatter_opts = {"color": "steelblue"} if spin == 0 else {"color": "teal"}
scatter_opts = dict(alpha=0.4, s=40, zorder=10)
items = (["fundamental_gaps", "direct_gaps"], ["in_state", "out_state"])
for i, (gap_name, state_name) in enumerate(itertools.product(*items)):
# Use getattr to extract gaps, equivalent to
#gap = self.fundamental_gaps[spin]
#e_start = gap.out_state.eig
items = list(enumerate(itertools.product(*items)))
for i, (gap_name, state_name) in items:
# Use getattr to extract gaps, equivalent to:
# gap = self.fundamental_gaps[spin]
# e_start = gap.out_state.eig
gap = getattr(self, gap_name)[spin]
e_start = getattr(gap, state_name).eig
#scatter_opts["marker"] = ["^", "v", "<", ">"][i]
scatter_opts["marker"] = "h"
scatter_opts["marker"] = "o"
scatter_opts["color"] = plt.get_cmap("cool" if spin == 0 else "summer")(i/len(items))
for band in range(self.mband):
eks = self.eigens[spin, :, band]
@ -2034,8 +2036,8 @@ class ElectronBands(Has_Structure):
return list(d.keys()), list(d.values())
@add_fig_kwargs
def plot_with_edos(self, edos, klabels=None, ax_list=None, e0="fermie", points=None, with_gaps=False,
ylims=None, width_ratios=(2, 1), **kwargs):
def plot_with_edos(self, edos, klabels=None, ax_list=None, e0="fermie", points=None,
with_gaps=False, max_phfreq=None, ylims=None, width_ratios=(2, 1), **kwargs):
r"""
Plot the band structure and the DOS.
@ -2061,7 +2063,12 @@ class ElectronBands(Has_Structure):
points: Marker object with the position and the size of the marker.
Used for plotting purpose e.g. QP energies, energy derivatives...
with_gaps: True to add marker and arrows showing the fundamental and the direct gap.
with_gaps: True to add markers and arrows showing the fundamental and the direct gap.
max_phfreq: Max phonon frequency in eV to activate scatterplot showing
possible phonon absorption/emission processes based on energy-conservation alone.
All final states whose energy is within +- max_phfreq of the initial state are included.
By default, the four electronic states defining the fundamental and the direct gaps
are considered as initial state (not available for metals).
width_ratios: Defines the ratio between the band structure plot and the dos plot.
Return: |matplotlib-Figure|
@ -2085,7 +2092,8 @@ class ElectronBands(Has_Structure):
#if not kwargs: kwargs = {"color": "black", "linewidth": 2.0}
# Plot the band structure
self.plot(e0=e0, ax=ax0, ylims=ylims, klabels=klabels, points=points, with_gaps=with_gaps, show=False)
self.plot(e0=e0, ax=ax0, ylims=ylims, klabels=klabels, points=points,
with_gaps=with_gaps, max_phfreq=max_phfreq, show=False)
# Plot the DOS
if self.nsppol == 1:
@ -2093,10 +2101,8 @@ class ElectronBands(Has_Structure):
edos.plot_ax(ax1, e0, exchange_xy=True, **opts)
else:
for spin in self.spins:
if spin == 0:
opts = {"color": "black", "linewidth": 2.0}
else:
opts = {"color": "red", "linewidth": 2.0}
opts = {"color": "black", "linewidth": 2.0} if spin == 0 else \
{"color": "red", "linewidth": 2.0}
edos.plot_ax(ax1, e0, spin=spin, exchange_xy=True, **opts)
ax1.grid(True)
@ -2744,7 +2750,12 @@ class ElectronBandsPlotter(NotebookWriter):
- None: Don't shift energies, equivalent to e0=0
with_dos: True if DOS should be printed.
with_gaps: True to add marker and arrows showing the fundamental and the direct gap.
with_gaps: True to add markesr and arrows showing the fundamental and the direct gap.
max_phfreq: Max phonon frequency in eV to activate scatterplot showing
possible phonon absorptions/emission processes based on energy-conservation alone.
All final states whose energy is within +- max_phfreq of the initial state are included.
By default, the four electronic states defining the fundamental and the direct gaps
are considered as initial state (not available for metals).
ylims: Set the data limits for the y-axis. Accept tuple e.g. ```(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used
fontsize: fontsize for titles and legend.
@ -2770,7 +2781,7 @@ class ElectronBandsPlotter(NotebookWriter):
for i, (ebands, ax) in enumerate(zip(ebands_list, ax_list)):
irow, icol = divmod(i, ncols)
ebands.plot(ax=ax, e0=e0, with_gaps=with_gaps, show=False)
ebands.plot(ax=ax, e0=e0, with_gaps=with_gaps, max_phfreq=max_phfreq, show=False)
set_axlims(ax, ylims, "y")
# This to handle with_gaps = True
title = ax.get_title()
@ -2794,7 +2805,8 @@ class ElectronBandsPlotter(NotebookWriter):
# Define the zero of energy and plot
mye0 = ebands.get_e0(e0) if e0 != "edos_fermie" else edos.fermie
ebands.plot_with_edos(edos, e0=mye0, ax_list=(ax0, ax1), with_gaps=with_gaps, show=False)
ebands.plot_with_edos(edos, e0=mye0, ax_list=(ax0, ax1), with_gaps=with_gaps,
max_phfreq=max_phfreq, show=False)
# This to handle with_gaps = True
title = ax0.get_title()
@ -3332,10 +3344,8 @@ class ElectronDos(object):
e0 = self.get_e0(e0)
for spin in range(self.nsppol):
if spin == 0:
opts = {"color": "black", "linewidth": 1.0}
else:
opts = {"color": "red", "linewidth": 1.0}
opts = {"color": "black", "linewidth": 1.0} if spin == 0 else \
{"color": "red", "linewidth": 1.0}
opts.update(kwargs)
spin_sign = +1 if spin == 0 else -1
x, y = self.spin_dos[spin].mesh - e0, spin_sign * self.spin_dos[spin].values
@ -3388,10 +3398,8 @@ class ElectronDos(object):
fig = ax_list[0].get_figure()
for spin in range(self.nsppol):
if spin == 0:
opts = {"color": "black", "linewidth": 1.0}
else:
opts = {"color": "red", "linewidth": 1.0}
opts = {"color": "black", "linewidth": 1.0} if spin == 0 else \
{"color": "red", "linewidth": 1.0}
# Plot Total dos if unpolarized.
if self.nsppol == 1: spin = None
self.plot_ax(ax_list[0], e0, spin=spin, what="idos", **opts)