def setUp(self):
with open(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"NaCl_phonon_bandstructure.json")) as f:
d = json.loads(f.read())
self.bs = PhononBandStructureSymmLine.from_dict(d)
self.plotter = PhononBSPlotter(self.bs)
def save_plot_band_structure(self,
filename,
img_format="eps",
units="thz",
ylim=None):
plotter = PhononBSPlotter(bs=self.phonon_band_structure_pymatgen)
plotter.save_plot(filename,
img_format=img_format,
units=units,
ylim=ylim)
class PhononBSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "NaCl_phonon_bandstructure.json"),
"r") as f:
d = json.loads(f.read())
self.bs = PhononBandStructureSymmLine.from_dict(d)
self.plotter = PhononBSPlotter(self.bs)
def test_bs_plot_data(self):
self.assertEqual(len(self.plotter.bs_plot_data()['distances'][0]), 51,
"wrong number of distances in the first branch")
self.assertEqual(len(self.plotter.bs_plot_data()['distances']), 4,
"wrong number of branches")
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()['distances']]),
204, "wrong number of distances")
self.assertEqual(self.plotter.bs_plot_data()['ticks']['label'][4], "Y",
"wrong tick label")
self.assertEqual(len(self.plotter.bs_plot_data()['ticks']['label']), 8,
"wrong number of tick labels")
def test_plot(self):
# Disabling latex for testing.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.get_plot(units="mev")
def test_plot_compare(self):
# Disabling latex for testing.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.plot_compare(self.plotter, units="mev")
def process_item(self, item):
mp_id = item['mp-id']
self.logger.debug("Processing {}".format(mp_id))
decoder = MontyDecoder()
ph_bs = decoder.process_decoded(item['ph_bs'])
web_doc = ph_bs.as_phononwebsite()
plotter = PhononBSPlotter(ph_bs)
ylim = (0, max(py_.flatten_deep(plotter.bs_plot_data()['frequency'])))
filelike = io.BytesIO()
plotter.save_plot(filelike, ylim=ylim, img_format="png")
image = Binary(filelike.getvalue())
filelike.close()
return dict(mp_id=mp_id, web_doc=web_doc, image=image)
class PhononBSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "NaCl_phonon_bandstructure.json"), "r") as f:
d = json.loads(f.read())
self.bs = PhononBandStructureSymmLine.from_dict(d)
self.plotter = PhononBSPlotter(self.bs)
def test_bs_plot_data(self):
self.assertEqual(len(self.plotter.bs_plot_data()['distances'][0]), 51,
"wrong number of distances in the first branch")
self.assertEqual(len(self.plotter.bs_plot_data()['distances']), 4,
"wrong number of branches")
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()['distances']]),
204, "wrong number of distances")
self.assertEqual(self.plotter.bs_plot_data()['ticks']['label'][4], "Y",
"wrong tick label")
self.assertEqual(len(self.plotter.bs_plot_data()['ticks']['label']),
8, "wrong number of tick labels")
def test_plot(self):
# Disabling latex for testing.
from matplotlib import rc
rc('text', usetex=False)
self.plotter.get_plot(units="mev")
class PhononBSPlotterTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "NaCl_phonon_bandstructure.json"),
"r") as f:
d = json.loads(f.read())
self.bs = PhononBandStructureSymmLine.from_dict(d)
self.plotter = PhononBSPlotter(self.bs)
def test_bs_plot_data(self):
self.assertEqual(len(self.plotter.bs_plot_data()['distances'][0]), 51,
"wrong number of distances in the first branch")
self.assertEqual(len(self.plotter.bs_plot_data()['distances']), 4,
"wrong number of branches")
self.assertEqual(
sum([len(e) for e in self.plotter.bs_plot_data()['distances']]),
204, "wrong number of distances")
self.assertEqual(self.plotter.bs_plot_data()['ticks']['label'][4], "Y",
"wrong tick label")
self.assertEqual(len(self.plotter.bs_plot_data()['ticks']['label']), 8,
"wrong number of tick labels")
def rms_kdep_plot(self, whichkpath=1, filename="rms.eps", format="eps"):
rms = self.rms_kdep()
if whichkpath == 1:
plotter = PhononBSPlotter(bs=self.bs1)
elif whichkpath == 2:
plotter = PhononBSPlotter(bs=self.bs2)
distances = []
for element in plotter.bs_plot_data()["distances"]:
distances.extend(element)
import matplotlib.pyplot as plt
plt.close("all")
plt.plot(distances, rms)
plt.xticks(ticks=plotter.bs_plot_data()["ticks"]["distance"],
labels=plotter.bs_plot_data()["ticks"]["label"])
plt.xlabel("Wave vector")
plt.ylabel("Phonons RMS (THz)")
plt.savefig(filename, format=format)
def runSimulation(self):
starting_struct = singleFromFile(self.args)
relaxed_struct = runCalc("all_relax", ["structures"],
[starting_struct], self.args)["structures"][0]
phonopy_struct = get_phonopy_structure(relaxed_struct)
supercell_matrix = 3 * eye(3)
phonon = Phonopy(phonopy_struct, supercell_matrix)
phonon.generate_displacements(distance=0.01)
supercells = phonon.supercells_with_displacements
phonon_structs = [get_pmg_structure(struct) for struct in supercells]
forces = runCalc("all_static", ["forces"], phonon_structs,
self.args)["forces"]
phonon.set_forces(array(forces))
phonon.produce_force_constants()
phonon.symmetrize_force_constants()
self.plotter = PhononBSPlotter(
get_phonon_band_structure_symm_line_from_fc(
relaxed_struct, supercell_matrix, phonon.force_constants))
def setUp(self):
with open(os.path.join(test_dir, "NaCl_phonon_bandstructure.json"), "r") as f:
d = json.loads(f.read())
self.bs = PhononBandStructureSymmLine.from_dict(d)
self.plotter = PhononBSPlotter(self.bs)
def __init__(self, bs, imag_tol=-5e-2):
PhononBSPlotter.__init__(self, bs)
self.imag_tol = imag_tol
def get_plot(self, units='THz', ymin=None, ymax=None, width=None,
height=None, dpi=None, plt=None, fonts=None, dos=None,
dos_aspect=3, color=None, style=None, no_base_style=False,
from_json=None, legend=None):
"""Get a :obj:`matplotlib.pyplot` object of the phonon band structure.
Args:
units (:obj:`str`, optional): Units of phonon frequency. Accepted
(case-insensitive) values are Thz, cm-1, eV, meV.
ymin (:obj:`float`, optional): The minimum energy on the y-axis.
ymax (:obj:`float`, optional): The maximum energy on the y-axis.
width (:obj:`float`, optional): The width of the plot.
height (:obj:`float`, optional): The height of the plot.
dpi (:obj:`int`, optional): The dots-per-inch (pixel density) for
the image.
fonts (:obj:`list`, optional): Fonts to use in the plot. Can be a
a single font, specified as a :obj:`str`, or several fonts,
specified as a :obj:`list` of :obj:`str`.
plt (:obj:`matplotlib.pyplot`, optional): A
:obj:`matplotlib.pyplot` object to use for plotting.
dos (:obj:`np.ndarray`): 2D Numpy array of total DOS data
dos_aspect (float): Width division for vertical DOS
color (:obj:`str` or :obj:`tuple`, optional): Line/fill colour in
any matplotlib-accepted format
style (:obj:`list`, :obj:`str`, or :obj:`dict`): Any matplotlib
style specifications, to be composed on top of Sumo base
style.
no_base_style (:obj:`bool`, optional): Prevent use of sumo base
style. This can make alternative styles behave more
predictably.
from_json (:obj:`list` or :obj:`None`, optional): List of paths to
:obj:`pymatgen.phonon.bandstructure.PhononBandStructureSymmline`
JSON dump files. These are used to generate additional plots
displayed under the data attached to this plotter.
The k-point path should be the same as the main plot; the
reciprocal lattice is adjusted to fit the scaling of the main
data input.
Returns:
:obj:`matplotlib.pyplot`: The phonon band structure plot.
"""
if from_json is None:
from_json = []
if legend is None:
legend = [''] * (len(from_json) + 1)
else:
if len(legend) == 1 + len(from_json):
pass
elif len(legend) == len(from_json):
legend = [''] + list(legend)
else:
raise ValueError('Inappropriate number of legend entries')
if color is None:
color = 'C0' # Default to first colour in matplotlib series
if dos is not None:
plt = pretty_subplot(1, 2, width=width, height=height,
sharex=False, sharey=True, dpi=dpi, plt=plt,
gridspec_kw={'width_ratios': [dos_aspect, 1],
'wspace': 0})
ax = plt.gcf().axes[0]
else:
plt = pretty_plot(width, height, dpi=dpi, plt=plt)
ax = plt.gca()
def _plot_lines(data, ax, color=None, alpha=1, zorder=1):
"""Pull data from any PhononBSPlotter and add to axis"""
dists = data['distances']
freqs = data['frequency']
# nd is branch index, nb is band index, nk is kpoint index
for nd, nb in itertools.product(range(len(data['distances'])),
range(self._nb_bands)):
f = freqs[nd][nb]
# plot band data
ax.plot(dists[nd], f, ls='-', c=color,
zorder=zorder)
data = self.bs_plot_data()
_plot_lines(data, ax, color=color)
for i, bs_json in enumerate(from_json):
with open(bs_json, 'rt') as f:
json_data = json.load(f)
json_data['lattice_rec'] = json.loads(
self._bs.lattice_rec.to_json())
bs = PhononBandStructureSymmLine.from_dict(json_data)
# bs.lattice_rec = self._bs.lattice_rec
# raise Exception(bs.qpoints)
json_plotter = PhononBSPlotter(bs)
json_data = json_plotter.bs_plot_data()
if json_plotter._nb_bands != self._nb_bands:
raise Exception('Number of bands in {} does not match '
'main plot'.format(bs_json))
_plot_lines(json_data, ax,
color='C{}'.format(i + 1),
zorder=0.5)
if any(legend): # Don't show legend if all entries are empty string
from matplotlib.lines import Line2D
ax.legend([Line2D([0], [0], color='C{}'.format(i))
for i in range(len(legend))],
legend)
self._maketicks(ax, units=units)
self._makeplot(ax, plt.gcf(), data, width=width, height=height,
ymin=ymin, ymax=ymax, dos=dos, color=color)
plt.tight_layout()
plt.subplots_adjust(wspace=0)
return plt
def setUp(self):
with open(os.path.join(test_dir, "NaCl_phonon_bandstructure.json"), "r") as f:
d = json.loads(f.read())
self.bs = PhononBandStructureSymmLine.from_dict(d)
self.plotter = PhononBSPlotter(self.bs)
def compare_plot(self, filename="band_comparison.eps", img_format="eps"):
plotter = PhononBSPlotter(bs=self.bs1)
plotter2 = PhononBSPlotter(bs=self.bs2)
new_plotter = plotter.plot_compare(plotter2)
new_plotter.savefig(filename, format=img_format)
new_plotter.close()
def plot_phonon_bands(self, filename = None, ylim=None, units='thz'):
bs = get_ph_bs_symm_line(os.path.join(self.wd, self.dfpt_folder+'/band.yaml'))
plotter = PhononBSPlotter(bs)
if filename==None:
filename = os.path.join(self.wd, self.dfpt_folder+'/'+self.kpath_name+'.eps')
plotter.save_plot(filename, ylim=ylim, units=units)