def phonon_bandplot(filename,
poscar=None,
prefix=None,
directory=None,
dim=None,
born=None,
qmesh=None,
spg=None,
primitive_axis=None,
line_density=60,
symprec=0.01,
mode='bradcrack',
kpt_list=None,
eigenvectors=False,
labels=None,
height=6.,
width=6.,
style=None,
no_base_style=False,
ymin=None,
ymax=None,
image_format='pdf',
dpi=400,
plt=None,
fonts=None,
dos=None):
"""A script to plot phonon band structure diagrams.
Args:
filename (str): Path to phonopy output. Can be a band structure yaml
file, ``FORCE_SETS``, ``FORCE_CONSTANTS``, or
``force_constants.hdf5``.
poscar (:obj:`str`, optional): Path to POSCAR file of unitcell. Not
required if plotting the phonon band structure from a yaml file. If
not specified, the script will search for a POSCAR file in the
current directory.
prefIx (:obj:`str`, optional): Prefix for file names.
directory (:obj:`str`, optional): The directory in which to save files.
born (:obj:`str`, optional): Path to file containing Born effective
charges. Should be in the same format as the file produced by the
``phonopy-vasp-born`` script provided by phonopy.
qmesh (:obj:`list` of :obj:`int`, optional): Q-point mesh to use for
calculating the density of state. Formatted as a 3x1 :obj:`list` of
:obj:`int`.
spg (:obj:`str` or :obj:`int`, optional): The space group international
number or symbol to override the symmetry determined by spglib.
This is not recommended and only provided for testing purposes.
This option will only take effect when ``mode = 'bradcrack'``.
primitive_matrix (:obj:`list`, optional): The transformation matrix
from the conventional to primitive cell. Only required when the
conventional cell was used as the starting structure. Should be
provided as a 3x3 :obj:`list` of :obj:`float`.
line_density (:obj:`int`, optional): Density of k-points along the
path.
mode (:obj:`str`, optional): Method used for calculating the
high-symmetry path. The options are:
bradcrack
Use the paths from Bradley and Cracknell. See [brad]_.
pymatgen
Use the paths from pymatgen. See [curt]_.
seekpath
Use the paths from SeeK-path. See [seek]_.
kpt_list (:obj:`list`, optional): List of k-points to use, formatted as
a list of subpaths, each containing a list of fractional k-points.
For example::
[ [[0., 0., 0.], [0., 0., 0.5]],
[[0.5, 0., 0.], [0.5, 0.5, 0.]] ]
Will return points along ``0 0 0 -> 0 0 1/2 | 1/2 0 0
-> 1/2 1/2 0``
path_labels (:obj:`list`, optional): The k-point labels. These should
be provided as a :obj:`list` of :obj:`str` for each subpath of the
overall path. For example::
[ ['Gamma', 'Z'], ['X', 'M'] ]
combined with the above example for ``kpt_list`` would indicate the
path: Gamma -> Z | X -> M. If no labels are provided, letters from
A -> Z will be used instead.
eigenvectors (:obj:`bool`, optional): Write the eigenvectors to the
yaml file.
dos (str): Path to Phonopy total dos .dat file
height (:obj:`float`, optional): The height of the plot.
width (:obj:`float`, optional): The width of the plot.
ymin (:obj:`float`, optional): The minimum energy on the y-axis.
ymax (:obj:`float`, optional): The maximum energy on the y-axis.
style (:obj:`list` or :obj:`str`, optional): (List of) 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.
image_format (:obj:`str`, optional): The image file format. Can be any
format supported by matplotlib, including: png, jpg, pdf, and svg.
Defaults to pdf.
dpi (:obj:`int`, optional): The dots-per-inch (pixel density) for
the image.
plt (:obj:`matplotlib.pyplot`, optional): A
:obj:`matplotlib.pyplot` object to use for plotting.
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`.
Returns:
A matplotlib pyplot object.
"""
if '.yaml' in filename:
yaml_file = filename
elif ('FORCE_SETS' == filename or 'FORCE_CONSTANTS' == filename
or '.hdf5' in filename):
try:
poscar = poscar if poscar else 'POSCAR'
poscar = Poscar.from_file(poscar)
except IOError:
msg = "Cannot find POSCAR file, cannot generate symmetry path."
logging.error("\n {}".format(msg))
sys.exit()
if not dim:
logging.info("Supercell size (--dim option) not provided.\n"
"Attempting to guess supercell dimensions.\n")
try:
sposcar = Poscar.from_file("SPOSCAR")
except IOError:
msg = "Could not determine supercell size (use --dim flag)."
logging.error("\n {}".format(msg))
sys.exit()
dim = (sposcar.structure.lattice.matrix *
poscar.structure.lattice.inv_matrix)
# round due to numerical noise error
dim = np.around(dim, 5)
elif np.array(dim).shape != (3, 3):
dim = np.diagflat(dim)
logging.info("Using supercell with dimensions:")
logging.info('\t' + str(dim).replace('\n', '\n\t') + '\n')
phonon = load_phonopy(filename,
poscar.structure,
dim,
symprec=symprec,
primitive_matrix=primitive_axis,
factor=VaspToTHz,
symmetrise=True,
born=born,
write_fc=False)
# calculate band structure
kpath, kpoints, labels = get_path_data(poscar.structure,
mode=mode,
symprec=symprec,
spg=spg,
kpt_list=kpt_list,
labels=labels,
phonopy=True)
# todo: calculate dos and plot also
# phonon.set_mesh(mesh, is_gamma_center=False, is_eigenvectors=True,
# is_mesh_symmetry=False)
# phonon.set_partial_DOS()
phonon.set_band_structure(kpoints, is_eigenvectors=eigenvectors)
yaml_file = 'sumo_band.yaml'
phonon._band_structure.write_yaml(labels=labels, filename=yaml_file)
else:
msg = "Do not recognise file type of {}".format(filename)
logging.error("\n {}".format(msg))
sys.exit()
save_files = False if plt else True # don't save if pyplot object provided
bs = get_ph_bs_symm_line(yaml_file,
has_nac=False,
labels_dict=kpath.kpoints)
# Replace dos filename with data array
if dos is not None:
if isfile(dos):
dos = np.genfromtxt(dos, comments='#')
elif dos:
phonon.set_mesh(qmesh,
is_gamma_center=False,
is_eigenvectors=True,
is_mesh_symmetry=False)
phonon.set_total_DOS()
dos_freq, dos_val = phonon.get_total_DOS()
dos = np.zeros((len(dos_freq), 2))
dos[:, 0], dos[:, 1] = dos_freq, dos_val
plotter = SPhononBSPlotter(bs)
plt = plotter.get_plot(ymin=ymin,
ymax=ymax,
height=height,
width=width,
plt=plt,
fonts=fonts,
dos=dos)
if save_files:
basename = 'phonon_band.{}'.format(image_format)
filename = '{}_{}'.format(prefix, basename) if prefix else basename
if directory:
filename = os.path.join(directory, filename)
if dpi is None:
dpi = rcParams['figure.dpi']
plt.savefig(filename,
format=image_format,
dpi=dpi,
bbox_inches='tight')
filename = save_data_files(bs, prefix=prefix, directory=directory)
else:
return plt
def _bs_from_filename(
filename,
poscar,
dim,
symprec,
spg,
kpt_list,
labels,
primitive_axis,
units,
born,
mode,
eigenvectors,
line_density,
):
"""Analyse input files to create band structure"""
if ".yaml" in filename:
logging.warning(
f"Reading pre-computed band structure from {filename}. "
"Be aware that many phonon-bandplot options will not "
"be relevant.")
yaml_file = filename
phonon = None
try:
poscar = poscar if poscar else "POSCAR"
poscar = Poscar.from_file(poscar)
except OSError:
msg = "Cannot find POSCAR file, cannot generate symmetry path."
logging.error(f"\n {msg}")
sys.exit()
elif ("FORCE_SETS" in filename or "FORCE_CONSTANTS" in filename
or ".hdf5" in filename):
try:
poscar = poscar if poscar else "POSCAR"
poscar = Poscar.from_file(poscar)
except OSError:
msg = "Cannot find POSCAR file, cannot generate symmetry path."
logging.error(f"\n {msg}")
sys.exit()
if not dim:
logging.info("Supercell size (--dim option) not provided.\n"
"Attempting to guess supercell dimensions.\n")
try:
sposcar = Poscar.from_file("SPOSCAR")
except OSError:
msg = "Could not determine supercell size (use --dim flag)."
logging.error(f"\n {msg}")
sys.exit()
dim = sposcar.structure.lattice.matrix @ poscar.structure.lattice.inv_matrix
# round due to numerical noise error
dim = np.around(dim, 5)
elif len(dim) == 9:
dim = np.array(dim).reshape(3, 3)
elif np.array(dim).shape != (3, 3):
dim = np.diagflat(dim)
logging.info("Using supercell with dimensions:")
logging.info("\t" + str(dim).replace("\n", "\n\t") + "\n")
factors = {
"ev": VaspToEv,
"thz": VaspToTHz,
"mev": VaspToEv * 1000,
"cm-1": VaspToCm,
}
phonon = load_phonopy(
filename,
poscar.structure,
dim,
primitive_matrix=primitive_axis,
factor=factors[units.lower()],
symmetrise=True,
born=born,
write_fc=False,
)
elif ".phonon" in filename:
logging.warning("Reading pre-computed band structure from CASTEP. "
"Be aware that many phonon-bandplot options will not "
"be relevant.")
castep_phonon = CastepPhonon.from_file(filename)
cell_file = ".".join(filename.split(".")[:-1] + ["cell"])
if isfile(cell_file):
logging.info(
f"Found .cell file, reading x-axis labels from {cell_file}")
castep_phonon.set_labels_from_file(cell_file)
else:
logging.warning("No .cell file found, cannot read x-axis labels.")
factors = {
"cm-1": 1.0,
"thz": 1 / THzToCm,
"ev": CmToEv,
"mev": 1000 * CmToEv
}
castep_phonon.frequencies *= factors[units.lower()]
bs = castep_phonon.get_band_structure()
return bs, None
else:
msg = f"Do not recognise file type of {filename}"
logging.error(f"\n {msg}")
sys.exit()
# calculate band structure
kpath, kpoints, labels = get_path_data(
poscar.structure,
mode=mode,
symprec=symprec,
spg=spg,
kpt_list=kpt_list,
labels=labels,
phonopy=True,
line_density=line_density,
)
# todo: calculate dos and plot also
# phonon.set_mesh(mesh, is_gamma_center=False, is_eigenvectors=True,
# is_mesh_symmetry=False)
# phonon.set_partial_DOS()
if ".yaml" not in filename:
phonon.run_band_structure(kpoints,
with_eigenvectors=eigenvectors,
labels=labels)
yaml_file = "sumo_band.yaml"
phonon.band_structure.write_yaml(filename=yaml_file)
bs = get_ph_bs_symm_line(yaml_file,
has_nac=False,
labels_dict=kpath.kpoints)
return bs, phonon
def _bs_from_filename(filename, poscar, dim, symprec, spg, kpt_list, labels,
primitive_axis, units, born, mode, eigenvectors):
"""Analyse input files to create band structure"""
if '.yaml' in filename:
yaml_file = filename
elif ('FORCE_SETS' in filename or 'FORCE_CONSTANTS' in filename
or '.hdf5' in filename):
try:
poscar = poscar if poscar else 'POSCAR'
poscar = Poscar.from_file(poscar)
except IOError:
msg = "Cannot find POSCAR file, cannot generate symmetry path."
logging.error("\n {}".format(msg))
sys.exit()
if not dim:
logging.info("Supercell size (--dim option) not provided.\n"
"Attempting to guess supercell dimensions.\n")
try:
sposcar = Poscar.from_file("SPOSCAR")
except IOError:
msg = "Could not determine supercell size (use --dim flag)."
logging.error("\n {}".format(msg))
sys.exit()
dim = (sposcar.structure.lattice.matrix *
poscar.structure.lattice.inv_matrix)
# round due to numerical noise error
dim = np.around(dim, 5)
elif len(dim) == 9:
dim = np.array(dim).reshape(3, 3)
elif np.array(dim).shape != (3, 3):
dim = np.diagflat(dim)
logging.info("Using supercell with dimensions:")
logging.info('\t' + str(dim).replace('\n', '\n\t') + '\n')
factors = {
'ev': VaspToEv,
'thz': VaspToTHz,
'mev': VaspToEv * 1000,
'cm-1': VaspToCm
}
phonon = load_phonopy(filename,
poscar.structure,
dim,
symprec=symprec,
primitive_matrix=primitive_axis,
factor=factors[units.lower()],
symmetrise=True,
born=born,
write_fc=False)
elif '.phonon' in filename:
logging.warning("Reading pre-computed band structure from CASTEP. "
"Be aware that many phonon-bandplot options will not "
"be relevant.")
castep_phonon = CastepPhonon.from_file(filename)
cell_file = '.'.join(filename.split('.')[:-1] + ['cell'])
if isfile(cell_file):
logging.info("Found .cell file, reading x-axis labels from "
"{}".format(cell_file))
castep_phonon.set_labels_from_file(cell_file)
else:
logging.warning("No .cell file found, cannot read x-axis labels.")
factors = {
'cm-1': 1.,
'thz': 1 / THzToCm,
'ev': CmToEv,
'mev': 1000 * CmToEv
}
castep_phonon.frequencies *= factors[units.lower()]
bs = castep_phonon.get_band_structure()
return bs, None
else:
msg = "Do not recognise file type of {}".format(filename)
logging.error("\n {}".format(msg))
sys.exit()
# calculate band structure
kpath, kpoints, labels = get_path_data(poscar.structure,
mode=mode,
symprec=symprec,
spg=spg,
kpt_list=kpt_list,
labels=labels,
phonopy=True)
# todo: calculate dos and plot also
# phonon.set_mesh(mesh, is_gamma_center=False, is_eigenvectors=True,
# is_mesh_symmetry=False)
# phonon.set_partial_DOS()
phonon.set_band_structure(kpoints,
is_eigenvectors=eigenvectors,
labels=labels)
yaml_file = 'sumo_band.yaml'
phonon._band_structure.write_yaml(filename=yaml_file)
bs = get_ph_bs_symm_line(yaml_file,
has_nac=False,
labels_dict=kpath.kpoints)
return bs, phonon