def test_plot_functions(self):
"""Testing plotting tools for phonons."""
phbst_filename = abidata.ref_file("trf2_5.out_PHBST.nc")
with abilab.abiopen(phbst_filename) as nc:
phbands = nc.phbands
phb_objects = [
phbands,
phbst_filename,
]
phdos_filename = abidata.ref_file("trf2_5.out_PHDOS.nc")
phdos = PhdosFile(phdos_filename)
phdos_objects = [
phdos,
phdos_filename,
]
if self.has_matplotlib():
assert phbands_gridplot(phb_objects,
titles=["phonons1", "phonons2"],
phdos_objects=phdos_objects,
units="meV",
show=False)
phdos.close()
def test_plot_functions(self):
"""Testing plotting tools for phonons."""
if not self.has_matplotlib():
raise unittest.SkipTest("matplotlib missing")
phbst_filename = abidata.ref_file("trf2_5.out_PHBST.nc")
from abipy import abilab
with abilab.abiopen(phbst_filename) as nc:
phbands = nc.phbands
phb_objects = [
phbands,
phbst_filename,
]
phdos_filename = abidata.ref_file("trf2_5.out_PHDOS.nc")
phdos = PhdosFile(phdos_filename)
phdos_objects = [
phdos,
phdos_filename,
]
fig = phbands_gridplot(phb_objects,
titles=["phonons1", "phonons2"],
phdos_objects=phdos_objects,
show=False)
assert fig is not None
phdos.close()
def test_from_phdosfile(self):
ncfile = PhdosFile(abidata.ref_file("trf2_5.out_PHDOS.nc"))
assert hasattr(ncfile, "structure")
phdos = ncfile.phdos
# Thermodinamics in the Harmonic approximation
#self.assert_almost_equal(phdos.zero_point_energy, )
f = phdos.get_free_energy()
#self.assert_almost_equal(f.values, )
u = phdos.get_internal_energy()
#self.assert_almost_equal(u.values, )
s = phdos.get_entropy()
#self.assert_almost_equal(s.values, )
cv = phdos.get_cv()
#self.assert_almost_equal(cv.values, )
if self.has_matplotlib():
ncfile.plot_pjdos_type(show=False)
phdos.plot(show=False)
phdos.plot_harmonic_thermo(tstar=20, tstop=350)
# Test notebook
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
ncfile.close()
def from_files(cls, gsr_paths, phdos_paths):
"""
Creates an instance of QHA from a list of GSR files and a list of PHDOS.nc files.
The list should have the same size and the volumes should match.
Args:
gsr_paths: list of paths to GSR files.
phdos_paths: list of paths to PHDOS.nc files.
Returns: A new instance of QHA
"""
energies = []
structures = []
for gp in gsr_paths:
with GsrFile.from_file(gp) as g:
energies.append(g.energy)
structures.append(g.structure)
#doses = [PhononDos.as_phdos(dp) for dp in phdos_paths]
doses = []
structures_from_phdos = []
for path in phdos_paths:
with PhdosFile(path) as p:
doses.append(p.phdos)
structures_from_phdos.append(p.structure)
cls._check_volumes(structures, structures_from_phdos)
return cls(structures, doses, energies)
def __init__(self,
ebands_kpath,
phbst_file,
phdos_file,
ebands_kmesh=None):
self.eb_kpath = ElectronBands.as_ebands(ebands_kpath)
self.eb_kmesh = ElectronBands.as_ebands(
ebands_kmesh) if ebands_kmesh is not None else None
self.phbst_file = phbst_file
if duck.is_string(self.phbst_file):
self.phbst_file = PhbstFile(self.phbst_file)
self.phb_qpath = self.phbst_file.phbands
self.phdos_file = phdos_file
if duck.is_string(self.phdos_file):
self.phdos_file = PhdosFile(phdos_file)
def test_plot_functions(self):
"""Testing plotting tools for phonons."""
phbst_filename = abidata.ref_file("trf2_5.out_PHBST.nc")
with abilab.abiopen(phbst_filename) as nc:
phbands = nc.phbands
phb_objects = [
phbands,
phbst_filename,
]
phdos_filename = abidata.ref_file("trf2_5.out_PHDOS.nc")
phdos = PhdosFile(phdos_filename)
phdos_objects = [
phdos,
phdos_filename,
]
if self.has_matplotlib():
assert phbands_gridplot(phb_objects, titles=["phonons1", "phonons2"],
phdos_objects=phdos_objects, units="meV", show=False)
phdos.close()
class EphPlotter(object):
"""
This object provides methods to plot electron and phonons for a single system.
An EphPlotter has:
- An |ElectronBands| on a k-path
- An |ElectronBands| on a k-mesh (optional)
- A |PhbstFile| with phonons along a q-path.
- A |PhdosFile| with different kinds of phonon DOSes.
EphPlotter uses these objects/files and other inputs/files provided by
the user to generate matplotlib plots related to e-ph interaction.
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: EphPlotter
"""
@classmethod
def from_ddb(cls, ddb, ebands_kpath, ebands_kmesh=None, **kwargs):
"""
Build the object from the ddb file, invoke anaddb to get phonon properties.
This entry point is needed to have phonon plots with LO-TO splitting
as AbiPy will generate an anaddb input with the different q --> 0 directions
required in phbands.plot to plot the LO-TO splitting correctly.
Args:
ddb: |DdbFile| or filepath.
ebands_kpath: |ElectronBands| with energies on a k-path or filepath.
ebands_kpath: (optional) |ElectronBands| with energies on a k-mesh or filepath.
kwargs: Passed to anaget_phbst_and_phdos_files
"""
ddb = DdbFile.as_ddb(ddb)
phbst_file, phdos_file = ddb.anaget_phbst_and_phdos_files(**kwargs)
return cls(ebands_kpath,
phbst_file,
phdos_file,
ebands_kmesh=ebands_kmesh)
def __init__(self,
ebands_kpath,
phbst_file,
phdos_file,
ebands_kmesh=None):
self.eb_kpath = ElectronBands.as_ebands(ebands_kpath)
self.eb_kmesh = ElectronBands.as_ebands(
ebands_kmesh) if ebands_kmesh is not None else None
self.phbst_file = phbst_file
if duck.is_string(self.phbst_file):
self.phbst_file = PhbstFile(self.phbst_file)
self.phb_qpath = self.phbst_file.phbands
self.phdos_file = phdos_file
if duck.is_string(self.phdos_file):
self.phdos_file = PhdosFile(phdos_file)
@add_fig_kwargs
def plot(self, eb_ylims=None, **kwargs):
"""
Plot electrons with possible (phonon-mediated) scattering channels for the CBM and VBM.
Also plot phonon band structure and phonon PJDOS.
Args:
eb_ylims: Set the data limits for the y-axis of the electron band. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If None, limits are selected automatically.
Return: |matplotlib-Figure|
"""
# Build grid. Share y-axis for Phbands and Phdos
import matplotlib.pyplot as plt
fig = plt.figure()
ax0 = plt.subplot2grid((3, 3), (0, 0), colspan=3, rowspan=2)
ax1 = plt.subplot2grid((3, 3), (2, 0), colspan=2, rowspan=1)
ax2 = plt.subplot2grid((3, 3), (2, 2), colspan=1, rowspan=1)
ax1.get_shared_y_axes().join(ax1, ax2)
# Plot electrons with possible e-ph scattering channels.
self.eb_kpath.plot(ax=ax0,
with_gaps=True,
ylims=eb_ylims,
max_phfreq=self.phb_qpath.maxfreq,
show=False)
# Plot phonon bands
self.phb_qpath.plot(ax=ax1, show=False)
#ax1.yaxis.set_visible(False)
#set_visible(ax1, False, "ylabel")
# Plot phonon PJDOS
self.phdos_file.plot_pjdos_type(ax=ax2,
fontsize=8,
exchange_xy=True,
show=False)
set_visible(ax2, False, "ylabel")
ax2.tick_params("y", left=False, labelleft=False)
ax2.tick_params("y", right=True, labelright=True)
# Adjust y-limits for phonons
ylims = self.phb_qpath.minfreq, self.phb_qpath.maxfreq + 0.1 * abs(
self.phb_qpath.maxfreq)
for ax in (ax1, ax2):
set_axlims(ax, ylims, "y")
return fig
@add_fig_kwargs
def plot_phonons_occ(self, temps=(100, 200, 300, 400), **kwargs):
"""
Plot phonon band structure with markers proportional to the occupation
of each phonon mode for different temperatures.
Args:
temps: List of temperatures in Kelvin.
Return: |matplotlib-Figure|
"""
temps = np.array(temps)
ntemp = len(temps)
# Build plot grid.
num_plots, ncols, nrows = ntemp, 1, 1
if num_plots > 1:
ncols = 2
nrows = (num_plots // ncols) + (num_plots % ncols)
ax_list, fig, plt = get_axarray_fig_plt(None,
nrows=nrows,
ncols=ncols,
sharex=True,
sharey=True,
squeeze=False)
ax_list = ax_list.ravel()
for ax, temp in zip(ax_list, temps.ravel()):
self.phb_qpath.plot(ax=ax,
units="eV",
temp=temp,
fontsize=8,
show=False)
return fig
@add_fig_kwargs
def plot_linewidths_sigeph(self, sigeph, eb_ylims=None, **kwargs):
"""
Plot e-bands + e-DOS + Im(Sigma_{eph}) + phonons + gkq^2
Args:
sigeph: |SigephFile| or string with path to file.
eb_ylims: Set the data limits for the y-axis of the electron band. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If None, limits are selected automatically.
"""
closeit = False
if duck.is_string(sigeph):
sigeph = SigEPhFile.from_file(sigeph)
closeit = True
# Build grid. share y-axis for Phbands and Phdos
import matplotlib.pyplot as plt
fig = plt.figure()
# Electrons
ax0 = plt.subplot2grid((2, 4), (0, 0), colspan=2, rowspan=1)
ax1 = plt.subplot2grid((2, 4), (0, 2), colspan=1, rowspan=1)
ax2 = plt.subplot2grid((2, 4), (0, 3), colspan=1, rowspan=1)
# Share y-axis
ax_share("y", ax0, ax1, ax2)
# Phonons
ax3 = plt.subplot2grid((2, 4), (1, 0), colspan=2, rowspan=1)
ax4 = plt.subplot2grid((2, 4), (1, 2), colspan=1, rowspan=1)
ax5 = plt.subplot2grid((2, 4), (1, 3), colspan=1, rowspan=1)
# Share y-axis
ax_share("y", ax3, ax4, ax5)
e0 = "fermie"
# Plot electrons with possible e-ph scattering channels.
self.eb_kpath.plot(ax=ax0,
e0=e0,
with_gaps=True,
ylims=eb_ylims,
max_phfreq=self.phb_qpath.maxfreq,
show=False)
sigeph.plot_lws_vs_e0(ax=ax1, e0=e0, exchange_xy=True, show=False)
sigeph.edos.plot(ax=ax2, e0=e0, exchange_xy=True, show=False)
# Plot phonon bands
self.phb_qpath.plot(ax=ax3, show=False)
sigeph.plot_a2fw_skb_sum(ax=ax4,
what="gkq2",
exchange_xy=True,
fontsize=8,
show=False)
# Plot phonon PJDOS
self.phdos_file.plot_pjdos_type(ax=ax5,
fontsize=8,
exchange_xy=True,
show=False)
#set_visible(ax4, False, "ylabel")
#ax4.tick_params("y", left=False, labelleft=False)
#ax4.tick_params("y", right=True, labelright=True)
if closeit: sigeph.close()
return fig
def test_from_phdosfile(self):
"""Testing PHDOS from netcdf file."""
ncfile = PhdosFile(abidata.ref_file("trf2_5.out_PHDOS.nc"))
repr(ncfile); str(ncfile)
assert ncfile.to_string(verbose=1)
assert hasattr(ncfile, "structure")
nw = len(ncfile.wmesh)
assert nw == 461
natom3 = len(ncfile.structure) * 3
# Read PJDOSes
assert list(ncfile.pjdos_symbol.keys()) == ["Al", "As"]
od = ncfile.reader.read_pjdos_symbol_xyz_dict()
assert list(od.keys()) == ["Al", "As"]
assert all(v.shape == (3, nw) for v in od.values())
arr = ncfile.reader.read_pjdos_atdir()
assert arr.shape == (len(ncfile.structure), 3, nw)
phdos = ncfile.phdos
# Test integrals of DOS (the tolerance is a bit low likely due to too coarse meshes)
self.assert_almost_equal(phdos.integral_value, natom3, decimal=1)
# Summing projected DOSes over types should give the total DOS.
pj_sum = sum(pjdos.integral_value for pjdos in ncfile.pjdos_symbol.values())
self.assert_almost_equal(phdos.integral_value, pj_sum)
# Summing projected DOSes over types and directions should give the total DOS.
# phdos_rc_type[ntypat, 3, nomega]
values = ncfile.reader.read_value("pjdos_rc_type").sum(axis=(0, 1))
tot_dos = abilab.Function1D(phdos.mesh, values)
self.assert_almost_equal(phdos.integral_value, tot_dos.integral_value)
assert phdos == PhononDos.as_phdos(abidata.ref_file("trf2_5.out_PHDOS.nc"))
# Test Thermodinamics in the Harmonic approximation
self.assert_almost_equal(phdos.zero_point_energy.to("Ha"), 0.0030872835637731303)
u = phdos.get_internal_energy()
self.assert_almost_equal(u.values[0], 0.084009326574073395)
self.assert_almost_equal(u.values[-1], 0.17270110252071791)
s = phdos.get_entropy()
self.assert_almost_equal(s.values[0], 1.6270193052583423e-08)
self.assert_almost_equal(s.values[-1], 0.00058238779354717)
cv = phdos.get_cv()
self.assert_almost_equal(cv.values[0], 5.3715488328604253e-08)
self.assert_almost_equal(cv.values[-1], 0.00045871909188672578)
f = phdos.get_free_energy()
self.assert_almost_equal(f.values, (u - s.mesh * s.values).values)
self.assertAlmostEqual(phdos.debye_temp, 469.01524830328606)
self.assertAlmostEqual(phdos.get_acoustic_debye_temp(len(ncfile.structure)), 372.2576492728813)
assert ncfile.to_pymatgen()
if self.has_matplotlib():
assert ncfile.plot_pjdos_type(show=False)
assert ncfile.plot_pjdos_type(units="cm-1", stacked=False, colormap="viridis", show=False)
assert ncfile.plot_pjdos_cartdirs_type(units="Thz", stacked=True, show=False)
assert ncfile.plot_pjdos_cartdirs_type(units="meV", stacked=False, alpha=0.5, show=False)
assert ncfile.plot_pjdos_cartdirs_site(units="meV", stacked=False, alpha=0.5, show=False)
assert ncfile.plot_pjdos_cartdirs_site(units="meV", view="all", stacked=True, alpha=0.5, show=False)
assert phdos.plot(units="cm-1", show=False)
assert phdos.plot_harmonic_thermo(tstar=20, tstop=350, units="eV", formula_units=1, show=False)
assert phdos.plot_harmonic_thermo(tstar=20, tstop=350, units="Jmol", formula_units=2, show=False)
# Test notebook
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
ncfile.close()
def test_from_phdosfile(self):
"""Testing PHDOS from netcdf file."""
ncfile = PhdosFile(abidata.ref_file("trf2_5.out_PHDOS.nc"))
repr(ncfile)
str(ncfile)
assert ncfile.to_string(verbose=1)
assert hasattr(ncfile, "structure")
nw = len(ncfile.wmesh)
assert nw == 461
natom3 = len(ncfile.structure) * 3
# Read PJDOSes
assert list(ncfile.pjdos_symbol.keys()) == ["Al", "As"]
od = ncfile.reader.read_pjdos_symbol_xyz_dict()
assert list(od.keys()) == ["Al", "As"]
assert all(v.shape == (3, nw) for v in od.values())
arr = ncfile.reader.read_pjdos_atdir()
assert arr.shape == (len(ncfile.structure), 3, nw)
phdos = ncfile.phdos
# Test integrals of DOS (the tolerance is a bit low likely due to too coarse meshes)
self.assert_almost_equal(phdos.integral_value, natom3, decimal=1)
# Summing projected DOSes over types should give the total DOS.
pj_sum = sum(pjdos.integral_value
for pjdos in ncfile.pjdos_symbol.values())
self.assert_almost_equal(phdos.integral_value, pj_sum)
# Summing projected DOSes over types and directions should give the total DOS.
# phdos_rc_type[ntypat, 3, nomega]
values = ncfile.reader.read_value("pjdos_rc_type").sum(axis=(0, 1))
tot_dos = abilab.Function1D(phdos.mesh, values)
self.assert_almost_equal(phdos.integral_value, tot_dos.integral_value)
assert phdos == PhononDos.as_phdos(
abidata.ref_file("trf2_5.out_PHDOS.nc"))
# Test Thermodinamics in the Harmonic approximation
self.assert_almost_equal(phdos.zero_point_energy.to("Ha"),
0.0030872835637731303)
u = phdos.get_internal_energy()
self.assert_almost_equal(u.values[0], 0.084009326574073395)
self.assert_almost_equal(u.values[-1], 0.17270110252071791)
s = phdos.get_entropy()
self.assert_almost_equal(s.values[0], 1.6270193052583423e-08)
self.assert_almost_equal(s.values[-1], 0.00058238779354717)
cv = phdos.get_cv()
self.assert_almost_equal(cv.values[0], 5.3715488328604253e-08)
self.assert_almost_equal(cv.values[-1], 0.00045871909188672578)
f = phdos.get_free_energy()
self.assert_almost_equal(f.values, (u - s.mesh * s.values).values)
self.assertAlmostEqual(phdos.debye_temp, 469.01524830328606)
self.assertAlmostEqual(
phdos.get_acoustic_debye_temp(len(ncfile.structure)),
372.2576492728813)
assert ncfile.to_pymatgen()
if self.has_matplotlib():
assert ncfile.plot_pjdos_type(show=False)
assert ncfile.plot_pjdos_type(units="cm-1",
stacked=False,
colormap="viridis",
show=False)
assert ncfile.plot_pjdos_type(units="eV",
stacked=True,
colormap="jet",
exchange_xy=True,
fontsize=8,
show=False)
assert ncfile.plot_pjdos_cartdirs_type(units="Thz",
stacked=True,
show=False)
assert ncfile.plot_pjdos_cartdirs_type(units="meV",
stacked=False,
alpha=0.5,
show=False)
assert ncfile.plot_pjdos_cartdirs_site(units="meV",
stacked=False,
alpha=0.5,
show=False)
assert ncfile.plot_pjdos_cartdirs_site(units="meV",
view="all",
stacked=True,
alpha=0.5,
show=False)
assert phdos.plot(units="cm-1", show=False)
assert phdos.plot_harmonic_thermo(tstar=20,
tstop=350,
units="eV",
formula_units=1,
show=False)
assert phdos.plot_harmonic_thermo(tstar=20,
tstop=350,
units="Jmol",
formula_units=2,
show=False)
# Test notebook
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
ncfile.close()