def test_interpolator(self):
"""Test QP interpolation."""
from abipy.abilab import abiopen, ElectronBandsPlotter
# Get quasiparticle results from the SIGRES.nc database.
sigres = abiopen(abidata.ref_file("si_g0w0ppm_nband30_SIGRES.nc"))
# Interpolate QP corrections and apply them on top of the KS band structures.
# QP band energies are returned in r.qp_ebands_kpath and r.qp_ebands_kmesh.
r = sigres.interpolate(
lpratio=5,
ks_ebands_kpath=abidata.ref_file("si_nscf_GSR.nc"),
ks_ebands_kmesh=abidata.ref_file("si_scf_GSR.nc"),
verbose=0,
filter_params=[1.0, 1.0],
line_density=10)
assert r.qp_ebands_kpath is not None
assert r.qp_ebands_kpath.kpoints.is_path
#print(r.qp_ebands_kpath.kpoints.ksampling, r.qp_ebands_kpath.kpoints.mpdivs_shifts)
assert r.qp_ebands_kpath.kpoints.mpdivs_shifts == (None, None)
assert r.qp_ebands_kmesh is not None
assert r.qp_ebands_kmesh.kpoints.is_ibz
assert r.qp_ebands_kmesh.kpoints.ksampling is not None
assert r.qp_ebands_kmesh.kpoints.is_mpmesh
qp_mpdivs, qp_shifts = r.qp_ebands_kmesh.kpoints.mpdivs_shifts
assert not ((qp_mpdivs, qp_shifts) == (None, None))
ks_mpdivs, ks_shifts = r.ks_ebands_kmesh.kpoints.mpdivs_shifts
self.assert_equal(qp_mpdivs, ks_mpdivs)
self.assert_equal(qp_shifts, ks_shifts)
# Get DOS from interpolated energies.
ks_edos = r.ks_ebands_kmesh.get_edos()
qp_edos = r.qp_ebands_kmesh.get_edos()
r.qp_ebands_kmesh.to_bxsf(self.get_tmpname(text=True))
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", r.ks_ebands_kpath, dos=ks_edos)
plotter.add_ebands("GW (interpolated)", r.qp_ebands_kpath, dos=qp_edos)
if self.has_matplotlib():
plotter.combiplot(title="Silicon band structure", show=False)
plotter.gridplot(title="Silicon band structure", show=False)
sigres.close()
def test_scissors_polyfit(self):
"""Testing scissors from SIGRES file."""
# Get the quasiparticle results from the SIGRES.nc database.
sigma_file = abiopen(abidata.ref_file("si_g0w0ppm_nband30_SIGRES.nc"))
qplist_spin = sigma_file.qplist_spin
sigma_file.close()
# Construct the scissors operator
domains = [[-10, 6.1], [6.1, 18]]
scissors = qplist_spin[0].build_scissors(domains, bounds=None)
# Read the KS band energies computed on the k-path
with abiopen(abidata.ref_file("si_nscf_GSR.nc")) as nc:
ks_bands = nc.ebands
# Read the KS band energies computed on the Monkhorst-Pack (MP) mesh
# and compute the DOS with the Gaussian method
with abiopen(abidata.ref_file("si_scf_GSR.nc")) as nc:
ks_mpbands = 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.
if self.has_matplotlib():
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_bands, dos=ks_dos)
plotter.add_ebands("LDA+scissors(e)", qp_bands, dos=qp_dos)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Silicon band structure")
plotter.gridplot(title="Silicon band structure")
#!/usr/bin/env python
"""
This example shows how to plot several band structures on a grid
We use two GSR files:
si_scf_GSR.n: energies on a homogeneous sampling of the BZ (can be used to compute DOS)
si_nscf_GSR.nc: energies on a k-path in the BZ (used to plot the band dispersion)
"""
from abipy.abilab import ElectronBandsPlotter
from abipy.data import ref_file
# To plot a grid with two band structures:
plotter = ElectronBandsPlotter()
plotter.add_ebands("BZ sampling", ref_file("si_scf_GSR.nc"))
plotter.add_ebands("k-path", ref_file("si_nscf_GSR.nc"))
frame = plotter.get_ebands_frame()
print(frame)
plotter.gridplot(e0=None)
#plotter.animate()
# To plot a grid with band structures + DOS, use the optional argument `edos_objects`
# The first subplot will get the band dispersion from eb_objects[0] and the dos from edos_objects[0]
# edos_kwargs is an optional dictionary with the arguments that will be passed to `get_dos` to compute the DOS.
#eb_objects = 2 * [ref_file("si_nscf_GSR.nc")]
#edos_objects = 2 * [ref_file("si_scf_GSR.nc")]
#plotter = ElectronBandsPlotter()
#plotter.add_ebands("Si", ref_file("si_nscf_GSR.nc"), dos=ref_file("si_scf_GSR.nc"))
#plotter.add_ebands("Same data", ref_file("si_nscf_GSR.nc"), dos=ref_file("si_scf_GSR.nc"))
#plotter.gridplot()
# Read the KS band energies computed on the k-path
ks_bands = abiopen(abidata.ref_file("si_nscf_GSR.nc")).ebands
# 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)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Silicon band structure")
plotter.gridplot(title="Silicon band structure")
sigma_file.close()
r = sigres.interpolate(lpratio=5,
ks_ebands_kpath=ks_ebands_kpath,
ks_ebands_kmesh=ks_ebands_kmesh)
qp_edos = r.qp_ebands_kmesh.get_edos()
# Shortcut: pass the name of the GSR files directly.
#r = sigres.interpolate(ks_ebands_kpath=abidata.ref_file("si_nscf_GSR.nc"),
# ks_ebands_kmesh=abidata.ref_file("si_scf_GSR.nc"))
#ks_edos = r.ks_ebands_kmesh.get_edos()
#qp_edos = r.qp_ebands_kmesh.get_edos()
# Use ElectronBandsPlotter to plot the KS and the QP band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_ebands_kpath, dos=ks_edos)
plotter.add_ebands("GW (interpolated)", r.qp_ebands_kpath, dos=qp_edos)
# Get pandas dataframe with band structure parameters.
#df = plotter.get_ebands_frame()
#print(df)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Combiplot")
plotter.boxplot(swarm=True, title="Boxplot")
plotter.combiboxplot(swarm=True, title="Combiboxplot")
# sphinx_gallery_thumbnail_number = 4
plotter.gridplot(title="Gridplot")
sigres.close()
We use two GSR files:
si_scf_GSR.n: energies on a homogeneous sampling of the BZ (can be used to compute DOS)
si_nscf_GSR.nc: energies on a k-path in the BZ (used to plot the band dispersion)
"""
from abipy.abilab import ElectronBandsPlotter
from abipy.data import ref_file
# To plot a grid with two band structures:
plotter = ElectronBandsPlotter()
plotter.add_ebands("BZ sampling", ref_file("si_scf_GSR.nc"))
plotter.add_ebands("k-path", ref_file("si_nscf_GSR.nc"))
# Get pandas dataframe
frame = plotter.get_ebands_frame()
print(frame)
plotter.gridplot()
#plotter.animate()
# To plot a grid with band structures + DOS, use the optional argument `edos_objects`
# The first subplot will get the band dispersion from eb_objects[0] and the DOS from edos_objects[0]
# edos_kwargs is an optional dictionary with the arguments that will be passed to `get_dos` to compute the DOS.
eb_objects = 2 * [ref_file("si_nscf_GSR.nc")]
edos_objects = 2 * [ref_file("si_scf_GSR.nc")]
plotter = ElectronBandsPlotter()
plotter.add_ebands("Si", ref_file("si_nscf_GSR.nc"), dos=ref_file("si_scf_GSR.nc"))
plotter.add_ebands("Same data", ref_file("si_nscf_GSR.nc"), dos=ref_file("si_scf_GSR.nc"))
plotter.gridplot()
# Read the KS band energies computed on the k-path
ks_bands = abiopen(abidata.ref_file("si_nscf_GSR.nc")).ebands
# 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_edos = 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_edos = qp_mpbands.get_edos()
# Plot the LDA and the QPState band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_bands, edos=ks_edos)
plotter.add_ebands("LDA+scissors(e)", qp_bands, edos=qp_edos)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Silicon band structure")
plotter.gridplot(title="Silicon band structure")
sigma_file.close()
# This part is optional
points = sigres.get_points_from_ebands(r.qp_ebands_kpath, size=24)
r.qp_ebands_kpath.plot(points=points, with_gaps=True)
#raise ValueError()
# Shortcut: pass the name of the GSR files directly.
#r = sigres.interpolate(ks_ebands_kpath=abidata.ref_file("si_nscf_GSR.nc"),
# ks_ebands_kmesh=abidata.ref_file("si_scf_GSR.nc"))
#ks_edos = r.ks_ebands_kmesh.get_edos()
#qp_edos = r.qp_ebands_kmesh.get_edos()
# Use ElectronBandsPlotter to plot the KS and the QP band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_ebands_kpath, edos=ks_edos)
plotter.add_ebands("GW (interpolated)", r.qp_ebands_kpath, edos=qp_edos)
# Get pandas dataframe with band structure parameters.
#df = plotter.get_ebands_frame()
#print(df)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Combiplot")
plotter.boxplot(swarm=True, title="Boxplot")
plotter.combiboxplot(swarm=True, title="Combiboxplot")
# sphinx_gallery_thumbnail_number = 4
plotter.gridplot(title="Gridplot", with_gaps=True)
sigres.close()
si_scf_GSR.n: energies on a homogeneous sampling of the BZ (can be used to compute DOS)
si_nscf_GSR.nc: energies on a k-path in the BZ (used to plot the band dispersion)
"""
from abipy.abilab import ElectronBandsPlotter
from abipy.data import ref_file
# To plot a grid with two band structures:
plotter = ElectronBandsPlotter()
plotter.add_ebands("BZ sampling", ref_file("si_scf_GSR.nc"))
plotter.add_ebands("k-path", ref_file("si_nscf_GSR.nc"))
# Get pandas dataframe
frame = plotter.get_ebands_frame()
print(frame)
plotter.gridplot(with_gaps=True)
#plotter.animate()
# To plot a grid with band structures + DOS, use the optional argument `edos_objects`
# The first subplot gets the band dispersion from eb_objects[0] and the DOS from edos_objects[0]
# edos_kwargs is an optional dictionary passed to `get_dos` to compute the DOS.
eb_objects = 2 * [ref_file("si_nscf_GSR.nc")]
edos_objects = 2 * [ref_file("si_scf_GSR.nc")]
# sphinx_gallery_thumbnail_number = 2
plotter = ElectronBandsPlotter()
plotter.add_ebands("Si",
ref_file("si_nscf_GSR.nc"),
edos=ref_file("si_scf_GSR.nc"))
plotter.add_ebands("Same data",
ref_file("si_nscf_GSR.nc"),
ks_ebands_kpath=ks_ebands_kpath,
ks_ebands_kmesh=ks_ebands_kmesh
)
qp_edos = r.qp_ebands_kmesh.get_edos()
# Shortcut: pass the name of the GSR files directly.
#r = sigres.interpolate(ks_ebands_kpath=abidata.ref_file("si_nscf_GSR.nc"),
# ks_ebands_kmesh=abidata.ref_file("si_scf_GSR.nc"))
#ks_edos = r.ks_ebands_kmesh.get_edos()
#qp_edos = r.qp_ebands_kmesh.get_edos()
# Use ElectronBandsPlotter to plot the KS and the QP band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_ebands_kpath, dos=ks_edos)
plotter.add_ebands("GW (interpolated)", r.qp_ebands_kpath, dos=qp_edos)
# Get pandas dataframe with band structure parameters.
#df = plotter.get_ebands_frame()
#print(df)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Combiplot")
plotter.boxplot(swarm=True, title="Boxplot")
plotter.combiboxplot(swarm=True, title="Combiboxplot")
# sphinx_gallery_thumbnail_number = 4
plotter.gridplot(title="Gridplot")
sigres.close()
# This part is optional
points = sigres.get_points_from_ebands(r.qp_ebands_kpath, size=24)
r.qp_ebands_kpath.plot(points=points, with_gaps=True)
#raise ValueError()
# Shortcut: pass the name of the GSR files directly.
#r = sigres.interpolate(ks_ebands_kpath=abidata.ref_file("si_nscf_GSR.nc"),
# ks_ebands_kmesh=abidata.ref_file("si_scf_GSR.nc"))
#ks_edos = r.ks_ebands_kmesh.get_edos()
#qp_edos = r.qp_ebands_kmesh.get_edos()
# Use ElectronBandsPlotter to plot the KS and the QP band structure with matplotlib.
plotter = ElectronBandsPlotter()
plotter.add_ebands("LDA", ks_ebands_kpath, edos=ks_edos)
plotter.add_ebands("GW (interpolated)", r.qp_ebands_kpath, edos=qp_edos)
# Get pandas dataframe with band structure parameters.
#df = plotter.get_ebands_frame()
#print(df)
# By default, the two band energies are shifted wrt to *their* fermi level.
# Use e=0 if you don't want to shift the eigenvalus
# so that it's possible to visualize the QP corrections.
plotter.combiplot(title="Combiplot")
plotter.boxplot(swarm=True, title="Boxplot")
plotter.combiboxplot(swarm=True, title="Combiboxplot")
# sphinx_gallery_thumbnail_number = 4
plotter.gridplot(title="Gridplot", with_gaps=True)
sigres.close()
si_scf_GSR.n: energies on a homogeneous sampling of the BZ (can be used to compute DOS)
si_nscf_GSR.nc: energies on a k-path in the BZ (used to plot the band dispersion)
"""
from abipy.abilab import ElectronBandsPlotter
from abipy.data import ref_file
# To plot a grid with two band structures:
plotter = ElectronBandsPlotter()
plotter.add_ebands("BZ sampling", ref_file("si_scf_GSR.nc"))
plotter.add_ebands("k-path", ref_file("si_nscf_GSR.nc"))
# Get pandas dataframe
frame = plotter.get_ebands_frame()
print(frame)
plotter.gridplot()
#plotter.animate()
# To plot a grid with band structures + DOS, use the optional argument `edos_objects`
# The first subplot gets the band dispersion from eb_objects[0] and the DOS from edos_objects[0]
# edos_kwargs is an optional dictionary passed to `get_dos` to compute the DOS.
eb_objects = 2 * [ref_file("si_nscf_GSR.nc")]
edos_objects = 2 * [ref_file("si_scf_GSR.nc")]
# sphinx_gallery_thumbnail_number = 2
plotter = ElectronBandsPlotter()
plotter.add_ebands("Si", ref_file("si_nscf_GSR.nc"), dos=ref_file("si_scf_GSR.nc"))
plotter.add_ebands("Same data", ref_file("si_nscf_GSR.nc"), dos=ref_file("si_scf_GSR.nc"))
plotter.gridplot()
