def test_decimation(self):
fs = FermiSurface.from_band_structure(self.band_structure, self.kpoint_dim)
n_faces_orig = len(fs.isosurfaces[Spin.up][0][1])
fs = FermiSurface.from_band_structure(
self.band_structure, self.kpoint_dim, decimate_factor=0.8
)
n_faces_new = len(fs.isosurfaces[Spin.up][0][1])
self.assertLess(n_faces_new, n_faces_orig)
def test_integration_wigner_seitz(self):
interpolater = Interpolater(self.band_structure)
new_bs, kpoint_dim = interpolater.interpolate_bands(1)
fs = FermiSurface.from_band_structure(new_bs, kpoint_dim)
plotter = FermiSurfacePlotter(fs)
plotter.plot(plot_type="mpl",
interactive=False,
filename=self.output_file)
def fsplot(
filename: Optional[Union[Path, str]] = None,
interpolate_factor: int = 8,
mu: float = 0.0,
wigner_seitz: bool = True,
spin: Optional[Spin] = None,
plot_type: str = "plotly",
interactive: bool = False,
prefix: Optional[str] = None,
directory: Optional[Union[Path, str]] = None,
image_format: str = "png",
dpi: float = 400,
):
"""Plot Fermi surfaces from a vasprun.xml file.
Args:
filename: Path to input vasprun file.
interpolate_factor: The factor by which to interpolate the bands.
mu: The level above the Fermi energy at which the isosurfaces are to be plotted.
wigner_seitz: Controls whether the cell is the Wigner-Seitz cell or the
reciprocal unit cell parallelepiped.
spin: The spin channel to plot. By default plots both spin channels.
plot_type: Method used for plotting. Valid options are: "matplotlib", "plotly",
"mayavi".
interactive: Whether to enable interactive plots.
prefix: Prefix for file names.
directory: The directory in which to save files.
image_format: The image file format.
dpi: The dots-per-inch (pixel density) for the image.
Returns:
The filename written to disk.
"""
from ifermi.fermi_surface import FermiSurface
from ifermi.interpolator import Interpolater
from ifermi.plotter import FSPlotter
if not filename:
filename = find_vasprun_file()
vr = Vasprun(filename)
bs = vr.get_band_structure()
interpolater = Interpolater(bs)
interp_bs, kpoint_dim = interpolater.interpolate_bands(interpolate_factor)
fs = FermiSurface.from_band_structure(
interp_bs, kpoint_dim, mu=mu, wigner_seitz=wigner_seitz, spin=spin,
)
plotter = FSPlotter(fs)
directory = directory if directory else "."
prefix = "{}_".format(prefix) if prefix else ""
output_filename = "{}fermi_surface.{}".format(prefix, image_format)
output_filename = Path(directory) / output_filename
plotter.plot(plot_type=plot_type, interactive=interactive, filename=output_filename)
from pathlib import Path
from monty.serialization import dumpfn
from ifermi.fermi_surface import FermiSurface
from ifermi.interpolator import Interpolater
from pymatgen.io.vasp.outputs import Vasprun
if __name__ == "__main__":
example_dir = Path("../../examples")
vr = Vasprun(example_dir / "MgB2/vasprun.xml")
bs = vr.get_band_structure()
dumpfn(bs.structure, "structure.json.gz")
interpolater = Interpolater(bs)
new_bs, kpoint_dim = interpolater.interpolate_bands(1)
bs_data = {"bs": new_bs, "dim": kpoint_dim, "structure": bs.structure}
dumpfn(bs_data, "bs_BaFe2As2.json.gz")
fs = FermiSurface.from_band_structure(new_bs, kpoint_dim, wigner_seitz=True)
dumpfn(fs, "fs_BaFe2As2_wigner.json.gz")
dumpfn(fs.reciprocal_space, "rs_wigner.json.gz")
fs = FermiSurface.from_band_structure(new_bs, kpoint_dim, wigner_seitz=False)
dumpfn(fs, "fs_BaFe2As2_reciprocal.json.gz")
dumpfn(fs.reciprocal_space, "rs_reciprocal.json.gz")
def test_reciprocal_cell(self):
fs = FermiSurface.from_band_structure(self.band_structure,
self.kpoint_dim,
wigner_seitz=False)
self.assert_fs_equal(fs, self.ref_fs_reciprocal)
def test_wigner_seitz_cell(self):
fs = FermiSurface.from_band_structure(self.band_structure,
self.kpoint_dim,
wigner_seitz=True)
self.assert_fs_equal(fs, self.ref_fs_wigner)
def fsplot2d(
filenames=None,
code="vasp",
prefix=None,
directory=None,
interpolate_factor=8,
mu=0.0,
image_format="pdf",
dpi=400,
plt=None,
fonts=None,
plane_orig=(0.0, 0.0, 0.5),
plane_norm=(0, 0, 1),
):
"""Plot electronic band structure diagrams from vasprun.xml files.
Args:
filenames (:obj:`str` or :obj:`list`, optional): Path to input files.
Vasp:
Use vasprun.xml or vasprun.xml.gz file.
If no filenames are provided, ifermi
will search for vasprun.xml or vasprun.xml.gz files in folders
named 'split-0*'. Failing that, the code will look for a vasprun in
the current directory.
code (:obj:`str`, optional): Calculation type. Default is 'vasp'
prefix (:obj:`str`, optional): Prefix for file names.
directory (:obj:`str`, optional): The directory in which to save files.
interpolate_factor (float, optional): The factor by which to interpolate the bands
mu (float, optional): The level above the Fermi energy at which the isosurfaces are to be
plotted.
image_format (:obj:`str`, optional): The image file format.
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.
Returns:
If ``plt`` set then the ``plt`` object will be returned. Otherwise, the
method will return a :obj:`list` of filenames written to disk.
"""
from ifermi.fermi_surface import FermiSurface
from ifermi.interpolator import Interpolater
from ifermi.plotter import FSPlotter, FSPlotter2D
if not filenames:
filenames = find_vasprun_files()
elif isinstance(filenames, str):
filenames = [filenames]
# # don't save if pyplot object provided
# save_files = False if plt else True
vr = Vasprun(filenames)
bs = vr.get_band_structure()
if not interpolate:
interpolate_factor = 1
interpolater = Interpolater(bs)
new_bs, hdims, rlattvec = interpolater.interpolate_bands(interpolate_factor)
fs = FermiSurface(new_bs, hdims, rlattvec, mu=mu, plot_wigner_seitz=False)
if plot_wigner_seitz:
bz = WignerSeitzCell(rlattvec)
rc = None
else:
bz = None
rc = RecipCell(rlattvec)
plotter = FSPlotter2D(fs, plane_orig=plane_orig, plane_norm=plane_norm)
plotter.fs2d_plot_data(plot_type="mpl")
def test_spin_up(self):
fs = FermiSurface.from_band_structure(
self.band_structure, self.kpoint_dim, spin=Spin.up
)
self.assert_fs_equal(fs, self.ref_fs_spin_up)
def fsplot(
filename: Optional[Union[Path, str]] = None,
interpolate_factor: int = 8,
mu: float = 0.0,
wigner_seitz: bool = True,
spin: Optional[Spin] = None,
plot_type: str = "plotly",
interactive: bool = False,
slice_info: Optional[Tuple[float, float, float, float]] = None,
prefix: Optional[str] = None,
directory: Optional[Union[Path, str]] = None,
image_format: str = "png",
dpi: float = 400,
):
"""Plot Fermi surfaces from a vasprun.xml file.
Args:
filename: Path to input vasprun file.
interpolate_factor: The factor by which to interpolate the bands.
mu: The level above the Fermi energy at which the isosurfaces are to be plotted.
wigner_seitz: Controls whether the cell is the Wigner-Seitz cell or the
reciprocal unit cell parallelepiped.
spin: The spin channel to plot. By default plots both spin channels.
plot_type: Method used for plotting. Valid options are: "matplotlib", "plotly",
"mayavi".
interactive: Whether to enable interactive plots.
prefix: Prefix for file names.
slice_info: Slice through the Brillouin zone. Given as the plane normal and
distance form the plane in fractional coordinates: E.g., ``[1, 0, 0, 0.2]``
where ``(1, 0, 0)`` are the miller indices and ``0.2`` is the distance from
the Gamma point.
directory: The directory in which to save files.
image_format: The image file format.
dpi: The dots-per-inch (pixel density) for the image.
Returns:
The filename written to disk.
"""
from ifermi.fermi_surface import FermiSurface
from ifermi.interpolator import Interpolater
from ifermi.plotter import FermiSurfacePlotter
if not filename:
filename = find_vasprun_file()
vr = Vasprun(filename)
bs = vr.get_band_structure()
interpolater = Interpolater(bs)
interp_bs, kpoint_dim = interpolater.interpolate_bands(interpolate_factor)
fs = FermiSurface.from_band_structure(
interp_bs, kpoint_dim, mu=mu, wigner_seitz=wigner_seitz
)
directory = directory if directory else "."
prefix = "{}_".format(prefix) if prefix else ""
if slice_info:
plane_normal = slice_info[:3]
distance = slice_info[3]
fermi_slice = fs.get_fermi_slice(plane_normal, distance)
plotter = FermiSlicePlotter(fermi_slice)
output_filename = "{}fermi_slice.{}".format(prefix, image_format)
output_filename = Path(directory) / output_filename
plotter.plot(filename=output_filename, spin=spin)
else:
plotter = FermiSurfacePlotter(fs)
output_filename = "{}fermi_surface.{}".format(prefix, image_format)
output_filename = Path(directory) / output_filename
plotter.plot(
plot_type=plot_type,
interactive=interactive,
filename=output_filename,
spin=spin,
)