def optplot(modes=('absorption', ),
filenames=None,
prefix=None,
directory=None,
gaussian=None,
band_gaps=None,
labels=None,
average=True,
height=6,
width=6,
xmin=0,
xmax=None,
ymin=0,
ymax=1e5,
colours=None,
style=None,
no_base_style=None,
image_format='pdf',
dpi=400,
plt=None,
fonts=None):
"""A script to plot optical absorption spectra from VASP calculations.
Args:
modes (:obj:`list` or :obj:`tuple`):
Ordered list of :obj:`str` determining properties to plot.
Accepted options are 'absorption' (default), 'eps', 'eps-real',
'eps-im', 'n', 'n-real', 'n-im', 'loss' (equivalent to n-im).
filenames (:obj:`str` or :obj:`list`, optional): Path to vasprun.xml
file (can be gzipped). Alternatively, a list of paths can be
provided, in which case the absorption spectra for each will be
plotted concurrently.
prefix (:obj:`str`, optional): Prefix for file names.
directory (:obj:`str`, optional): The directory in which to save files.
gaussian (:obj:`float`): Standard deviation for gaussian broadening.
band_gaps (:obj:`float` or :obj:`list`, optional): The band gap as a
:obj:`float`, plotted as a dashed line. If plotting multiple
spectra then a :obj:`list` of band gaps can be provided.
labels (:obj:`str` or :obj:`list`): A label to identify the spectra.
If plotting multiple spectra then a :obj:`list` of labels can
be provided.
average (:obj:`bool`, optional): Average the dielectric response across
all lattice directions. Defaults to ``True``.
height (:obj:`float`, optional): The height of the plot.
width (:obj:`float`, optional): The width of the plot.
xmin (:obj:`float`, optional): The minimum energy on the x-axis.
xmax (:obj:`float`, optional): The maximum energy on the x-axis.
ymin (:obj:`float`, optional): The minimum absorption intensity on the
y-axis.
ymax (:obj:`float`, optional): The maximum absorption intensity on the
y-axis.
colours (:obj:`list`, optional): A :obj:`list` of colours to use in the
plot. The colours can be specified as a hex code, set of rgb
values, or any other format supported by matplotlib.
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 not filenames:
if os.path.exists('vasprun.xml'):
filenames = ['vasprun.xml']
elif os.path.exists('vasprun.xml.gz'):
filenames = ['vasprun.xml.gz']
else:
logging.error('ERROR: No vasprun.xml found!')
sys.exit()
elif isinstance(filenames, str):
filenames = [filenames]
vrs = [Vasprun(f) for f in filenames]
dielectrics = [vr.dielectric for vr in vrs]
if gaussian:
dielectrics = [broaden_eps(d, gaussian) for d in dielectrics]
# initialize spectrum data ready to append from each dataset
abs_data = OrderedDict()
for mode in modes:
abs_data.update({mode: []})
# for each calculation, get all required properties and append to data
for d in dielectrics:
for mode, spectrum in calculate_dielectric_properties(
d, set(modes), average=average).items():
abs_data[mode].append(spectrum)
if isinstance(band_gaps, list) and not band_gaps:
# empty list therefore get bandgap from vasprun files
band_gaps = [
vr.get_band_structure().get_band_gap()['energy'] for vr in vrs
]
elif isinstance(band_gaps, list) and 'vasprun' in band_gaps[0]:
# band_gaps contains list of vasprun files
bg_vrs = [Vasprun(f) for f in band_gaps]
band_gaps = [
vr.get_band_structure().get_band_gap()['energy'] for vr in bg_vrs
]
elif isinstance(band_gaps, list):
# band_gaps is non empty list w. no vaspruns; presume floats
band_gaps = [float(i) for i in band_gaps]
save_files = False if plt else True
if len(abs_data) > 1 and not labels:
labels = [
latexify(vr.final_structure.composition.reduced_formula).replace(
'$_', '$_\mathregular') for vr in vrs
]
plotter = SOpticsPlotter(abs_data, band_gap=band_gaps, label=labels)
plt = plotter.get_plot(width=width,
height=height,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
colours=colours,
dpi=dpi,
plt=plt,
fonts=fonts,
style=style,
no_base_style=no_base_style)
if save_files:
basename = 'absorption'
if prefix:
basename = '{}_{}'.format(prefix, basename)
image_filename = '{}.{}'.format(basename, image_format)
if directory:
image_filename = os.path.join(directory, image_filename)
plt.savefig(image_filename, format=image_format, dpi=dpi)
for mode, data in abs_data.items():
basename = 'absorption' if mode == 'abs' else mode
write_files(data,
basename=basename,
prefix=prefix,
directory=directory)
else:
return plt
def optplot(
modes=("absorption", ),
filenames=None,
codes="vasp",
prefix=None,
directory=None,
gaussian=None,
band_gaps=None,
labels=None,
average=True,
height=6,
width=6,
xmin=0,
xmax=None,
ymin=0,
ymax=1e5,
colours=None,
style=None,
no_base_style=None,
image_format="pdf",
dpi=400,
plt=None,
fonts=None,
units="eV",
):
"""A script to plot optical absorption spectra from VASP calculations.
Args:
modes (:obj:`list` or :obj:`tuple`):
Ordered list of :obj:`str` determining properties to plot.
Accepted options are 'absorption' (default), 'eps', 'eps-real',
'eps-im', 'n', 'n-real', 'n-im', 'loss' (equivalent to n-im).
filenames (:obj:`str` or :obj:`list`, optional): Path to data file.
For VASP this is a *vasprun.xml* file (can be gzipped); for
Questaal the *opt.ext* file from *lmf* or *eps_BSE.out* from
*bethesalpeter* may be used.
Alternatively, a list of paths can be
provided, in which case the absorption spectra for each will be
plotted concurrently.
codes (:obj:`str` or :obj:`list`, optional): Original
calculator. Accepted values are 'vasp' and 'questaal'. Items should
correspond to filenames.
prefix (:obj:`str`, optional): Prefix for file names.
directory (:obj:`str`, optional): The directory in which to save files.
gaussian (:obj:`float`): Standard deviation for gaussian broadening.
band_gaps (:obj:`float`, :obj:`str` or :obj:`list`, optional): The band
gap as a :obj:`float`, in eV, plotted as a dashed line. If plotting
multiple spectra then a :obj:`list` of band gaps can be provided.
Band gaps can be provided as a floating-point number or as a path
to a *vasprun.xml* file. To skip over a line, set its bandgap to
zero or a negative number to place it outside the visible range.
labels (:obj:`str` or :obj:`list`): A label to identify the spectra.
If plotting multiple spectra then a :obj:`list` of labels can
be provided.
average (:obj:`bool`, optional): Average the dielectric response across
all lattice directions. Defaults to ``True``.
height (:obj:`float`, optional): The height of the plot.
width (:obj:`float`, optional): The width of the plot.
xmin (:obj:`float`, optional): The minimum energy on the x-axis.
xmax (:obj:`float`, optional): The maximum energy on the x-axis.
ymin (:obj:`float`, optional): The minimum absorption intensity on the
y-axis.
ymax (:obj:`float`, optional): The maximum absorption intensity on the
y-axis.
colours (:obj:`list`, optional): A :obj:`list` of colours to use in the
plot. The colours can be specified as a hex code, set of rgb
values, or any other format supported by matplotlib.
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`.
units (:obj:`str`, optional): X-axis units for the plot. 'eV' for
energy in electronvolts or 'nm' for wavelength in nanometers.
Defaults to 'eV'.
Returns:
A matplotlib pyplot object.
"""
# Don't write files if this is being done to manipulate existing plt
save_files = False if plt else True
# BUILD LIST OF FILES AUTOMATICALLY IF NECESSARY
if codes == "vasp":
if not filenames:
if os.path.exists("vasprun.xml"):
filenames = ["vasprun.xml"]
elif os.path.exists("vasprun.xml.gz"):
filenames = ["vasprun.xml.gz"]
else:
logging.error("ERROR: No vasprun.xml found!")
sys.exit()
elif codes == "questaal":
if not filenames:
if len(glob("opt.*")) > 0:
filenames = glob("opt.*")
if len(filenames) == 1:
logging.info("Found optics file: " + filenames[0])
else:
logging.info("Found optics files: " + ", ".join(filenames))
if isinstance(filenames, str):
filenames = [filenames]
if isinstance(codes, str):
codes = [codes] * len(filenames)
elif len(codes) == 1:
codes = list(codes) * len(filenames)
# ITERATE OVER FILES READING DIELECTRIC DATA
dielectrics = []
auto_labels = []
auto_band_gaps = []
for i, (filename, code) in enumerate(zip(filenames, codes)):
if code == "vasp":
vr = Vasprun(filename)
dielectrics.append(vr.dielectric)
auto_labels.append(
latexify(
vr.final_structure.composition.reduced_formula).replace(
"$_", r"$_\mathregular"))
if isinstance(band_gaps, list) and not band_gaps:
# band_gaps = [], auto band gap requested
auto_band_gaps.append(
vr.get_band_structure().get_band_gap()["energy"])
else:
auto_band_gaps.append(None)
elif code == "questaal":
if not save_files:
out_filename = None
elif len(filenames) == 1:
out_filename = "dielectric.dat"
else:
out_filename = f"dielectric_{i + 1}.dat"
dielectrics.append(
questaal.dielectric_from_file(filename, out_filename))
auto_band_gaps.append(None)
auto_labels.append(filename.split(".")[-1])
if isinstance(band_gaps, list) and not band_gaps:
logging.info("Bandgap requested but not supported for Questaal"
" file {}: skipping...".format(filename))
else:
raise Exception(f'Code selection "{code}" not recognised')
if not labels and len(filenames) > 1:
labels = auto_labels
# PROCESS DIELECTRIC DATA: BROADENING AND DERIVED PROPERTIES
if gaussian:
dielectrics = [broaden_eps(d, gaussian) for d in dielectrics]
# initialize spectrum data ready to append from each dataset
abs_data = OrderedDict()
for mode in modes:
abs_data.update({mode: []})
# for each calculation, get all required properties and append to data
for d in dielectrics:
# TODO: add support for other eigs and full modes
energies, properties = calculate_dielectric_properties(
d, set(modes), mode="average" if average else "trace")
for mode, spectrum in properties.items():
abs_data[mode].append((energies, spectrum))
if isinstance(band_gaps, list) and not band_gaps:
# empty list therefore use bandgaps collected from vasprun files
band_gaps = auto_band_gaps
elif isinstance(band_gaps, list):
# list containing filenames and/or values: mutate the list in-place
for i, item in enumerate(band_gaps):
if item is None:
pass
elif _floatable(item):
band_gaps[i] = float(item)
elif "vasprun" in item:
band_gaps[i] = (Vasprun(
item).get_band_structure().get_band_gap()["energy"])
else:
raise ValueError(
f"Format not recognised for auto bandgap: {item}.")
plotter = SOpticsPlotter(abs_data, band_gap=band_gaps, label=labels)
plt = plotter.get_plot(
width=width,
height=height,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
colours=colours,
dpi=dpi,
plt=plt,
fonts=fonts,
style=style,
no_base_style=no_base_style,
units=units,
)
if save_files:
basename = "absorption"
if prefix:
basename = f"{prefix}_{basename}"
image_filename = f"{basename}.{image_format}"
if directory:
image_filename = os.path.join(directory, image_filename)
plt.savefig(image_filename, format=image_format, dpi=dpi)
for mode, data in abs_data.items():
basename = "absorption" if mode == "abs" else mode
write_files(data,
basename=basename,
prefix=prefix,
directory=directory)
else:
return plt
def optplot(filenames=None,
prefix=None,
directory=None,
gaussian=None,
band_gaps=None,
labels=None,
average=True,
height=6,
width=6,
xmin=0,
xmax=None,
ymin=0,
ymax=1e5,
colours=None,
image_format='pdf',
dpi=400,
plt=None,
fonts=None):
"""A script to plot optical absorption spectra from VASP calculations.
Args:
filenames (:obj:`str` or :obj:`list`, optional): Path to vasprun.xml
file (can be gzipped). Alternatively, a list of paths can be
provided, in which case the absorption spectra for each will be
plotted concurrently.
prefix (:obj:`str`, optional): Prefix for file names.
directory (:obj:`str`, optional): The directory in which to save files.
gaussian (:obj:`float`): Standard deviation for gaussian broadening.
band_gaps (:obj:`float` or :obj:`list`, optional): The band gap as a
:obj:`float`, plotted as a dashed line. If plotting multiple
spectra then a :obj:`list` of band gaps can be provided.
labels (:obj:`str` or :obj:`list`): A label to identify the spectra.
If plotting multiple spectra then a :obj:`list` of labels can
be provided.
average (:obj:`bool`, optional): Average the dielectric response across
all lattice directions. Defaults to ``True``.
height (:obj:`float`, optional): The height of the plot.
width (:obj:`float`, optional): The width of the plot.
xmin (:obj:`float`, optional): The minimum energy on the x-axis.
xmax (:obj:`float`, optional): The maximum energy on the x-axis.
ymin (:obj:`float`, optional): The minimum absorption intensity on the
y-axis.
ymax (:obj:`float`, optional): The maximum absorption intensity on the
y-axis.
colours (:obj:`list`, optional): A :obj:`list` of colours to use in the
plot. The colours can be specified as a hex code, set of rgb
values, or any other format supported by matplotlib.
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 not filenames:
if os.path.exists('vasprun.xml'):
filenames = ['vasprun.xml']
elif os.path.exists('vasprun.xml.gz'):
filenames = ['vasprun.xml.gz']
else:
logging.error('ERROR: No vasprun.xml found!')
sys.exit()
elif type(filenames) is str:
filenames = [filenames]
vrs = [Vasprun(f) for f in filenames]
dielectrics = [vr.dielectric for vr in vrs]
if gaussian:
dielectrics = [broaden_eps(d, gaussian) for d in dielectrics]
abs_data = [calculate_alpha(d, average=average) for d in dielectrics]
if type(band_gaps) is list and not band_gaps:
# empty list therefore get bandgap from vasprun files
band_gaps = [
vr.get_band_structure().get_band_gap()['energy'] for vr in vrs
]
elif type(band_gaps) is list and 'vasprun' in band_gaps[0]:
# band_gaps contains list of vasprun files
bg_vrs = [Vasprun(f) for f in band_gaps]
band_gaps = [
vr.get_band_structure().get_band_gap()['energy'] for vr in bg_vrs
]
elif type(band_gaps) is list:
# band_gaps is non empty list w. no vaspruns; presume floats
band_gaps = [float(i) for i in band_gaps]
save_files = False if plt else True
if len(abs_data) > 1 and not labels:
labels = [
latexify(vr.final_structure.composition.reduced_formula).replace(
'$_', '$_\mathregular') for vr in vrs
]
plotter = SOpticsPlotter(abs_data, band_gap=band_gaps, label=labels)
plt = plotter.get_plot(width=width,
height=height,
xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
colours=colours,
dpi=dpi,
plt=plt,
fonts=fonts)
if save_files:
basename = 'absorption.{}'.format(image_format)
filename = '{}_{}'.format(prefix, basename) if prefix else basename
if directory:
filename = os.path.join(directory, filename)
plt.savefig(filename, format=image_format, dpi=dpi)
write_files(abs_data, prefix=prefix, directory=directory)
else:
return plt