def test_phbands_plotter(self):
"""Testing phbands plotter."""
phbst_paths = 2 * [abidata.ref_file("trf2_5.out_PHBST.nc")]
phdos_paths = 2 * [abidata.ref_file("trf2_5.out_PHDOS.nc")]
plotter = PhononBandsPlotter()
plotter.add_phbands("AlAs", phbst_paths[0], phdos=phdos_paths[0])
plotter.add_phbands("Same-AlAs", phbst_paths[1], phdos=phdos_paths[1])
repr(plotter)
str(plotter)
assert len(plotter.phbands_list) == 2
assert len(plotter.phdoses_list) == 2
assert plotter.has_same_formula()
# __add__ merges two plotters:
p2 = plotter.add_plotter(plotter)
assert len(p2.phbands_list) == 2
assert len(p2.phdoses_list) == 2
df = dataframe_from_phbands(plotter.phbands_list)
assert "nqpt" in df
df = plotter.get_phbands_frame()
assert df is not None
if self.has_matplotlib():
assert plotter.combiplot(units="eV", show=True)
assert plotter.gridplot(units="meV", show=True)
assert plotter.boxplot(units="cm-1", show=True)
assert plotter.combiboxplot(units="Thz", show=True)
assert plotter.animate(show=False)
if self.has_nbformat():
plotter.write_notebook(nbpath=self.get_tmpname(text=True))
if self.has_ipywidgets():
assert plotter.ipw_select_plot() is not None
# Plotter without PHDOS
plotter = PhononBandsPlotter(
key_phbands=[("foo", phbst_paths[0]), ("bar", phbst_paths[1])])
if self.has_matplotlib():
assert plotter.combiplot(units="EV", show=True)
assert plotter.gridplot(units="MEV", show=True)
assert plotter.boxplot(units="cm^-1",
mode_range=[0, 3],
swarm=True,
show=True)
assert plotter.combiboxplot(units="THZ",
mode_range=[0, 3],
show=True)
def test_phbands_plotter(self):
"""Testing phbands plotter."""
phbst_paths = 2 * [abidata.ref_file("trf2_5.out_PHBST.nc")]
phdos_paths = 2 * [abidata.ref_file("trf2_5.out_PHDOS.nc")]
plotter = PhononBandsPlotter()
plotter.add_phbands("AlAs", phbst_paths[0], phdos=phdos_paths[0])
plotter.add_phbands("Same-AlAs", phbst_paths[1], phdos=phdos_paths[1])
repr(plotter); str(plotter)
assert len(plotter.phbands_list) == 2
assert len(plotter.phdoses_list) == 2
assert plotter.has_same_formula()
# __add__ merges two plotters:
p2 = plotter.add_plotter(plotter)
assert len(p2.phbands_list) == 2
assert len(p2.phdoses_list) == 2
df = dataframe_from_phbands(plotter.phbands_list)
assert "nqpt" in df
df = plotter.get_phbands_frame()
assert df is not None
if self.has_matplotlib():
assert plotter.combiplot(units="eV", show=True)
assert plotter.gridplot(units="meV", show=True)
assert plotter.boxplot(units="cm-1", show=True)
assert plotter.combiboxplot(units="Thz", show=True)
assert plotter.animate(show=False)
if self.has_nbformat():
plotter.write_notebook(nbpath=self.get_tmpname(text=True))
if self.has_ipywidgets():
assert plotter.ipw_select_plot() is not None
# Plotter without PHDOS
plotter = PhononBandsPlotter(key_phbands=[("foo", phbst_paths[0]), ("bar", phbst_paths[1])])
if self.has_matplotlib():
assert plotter.combiplot(units="EV", show=True)
assert plotter.gridplot(units="MEV", show=True)
assert plotter.boxplot(units="cm^-1", mode_range=[0, 3], swarm=True, show=True)
assert plotter.combiboxplot(units="THZ", mode_range=[0, 3], show=True)
def plot_phbs(self,
phbands,
temperatures=None,
t_max=1000,
colormap="plasma",
**kwargs):
"""
Given a list of |PhononBands| plots the band structures with a color depending on
the temperature using a |PhononBandsPlotter|.
If temperatures are not given they will be deduced inverting the dependence of volume
with respect to the temperature. If a unique volume could not be identified an error will
be raised.
Args:
phbands: list of |PhononBands| objects.
temperatures: list of temperatures.
t_max: maximum temperature considered for plotting.
colormap: matplotlib color map.
Returns: |matplotlib-Figure|
"""
if temperatures is None:
tv = self.get_t_for_vols([b.structure.volume for b in phbands],
t_max=t_max)
temperatures = []
for b, t in zip(phbands, tv):
if len(t) != 1:
raise ValueError(
"Couldn't find a single temperature for structure with "
"volume {}. Found {}: {}".format(
b.structure.volume, len(t), list(t)))
temperatures.append(t[0])
temperatures_str = ["{:.0f} K".format(t) for t in temperatures]
import matplotlib.pyplot as plt
cmap = plt.get_cmap(colormap)
colors = [cmap(t / max(temperatures)) for t in temperatures]
labels_phbs = zip(temperatures_str, phbands)
pbp = PhononBandsPlotter(labels_phbs)
pbp._LINE_COLORS = colors
pbp._LINE_STYLES = ['-']
fig = pbp.combiplot(show=False, **kwargs)
return fig
def plot_phbs(self, phbands, temperatures=None, t_max=1000, colormap="plasma", **kwargs):
"""
Given a list of |PhononBands| plots the band structures with a color depending on
the temperature using a |PhononBandsPlotter|.
If temperatures are not given they will be deduced inverting the dependence of volume
with respect to the temperature. If a unique volume could not be identified an error will
be raised.
Args:
phbands: list of |PhononBands| objects.
temperatures: list of temperatures.
t_max: maximum temperature considered for plotting.
colormap: matplotlib color map.
Returns: |matplotlib-Figure|
"""
if temperatures is None:
tv = self.get_t_for_vols([b.structure.volume for b in phbands], t_max=t_max)
temperatures = []
for b, t in zip(phbands, tv):
if len(t) != 1:
raise ValueError("Couldn't find a single temperature for structure with "
"volume {}. Found {}: {}".format(b.structure.volume, len(t), list(t)))
temperatures.append(t[0])
temperatures_str = ["{:.0f} K".format(t) for t in temperatures]
import matplotlib.pyplot as plt
cmap = plt.get_cmap(colormap)
colors = [cmap(t / max(temperatures)) for t in temperatures]
labels_phbs = zip(temperatures_str, phbands)
pbp = PhononBandsPlotter(labels_phbs)
pbp._LINE_COLORS = colors
pbp._LINE_STYLES = ['-']
fig = pbp.combiplot(show=False, **kwargs)
return fig