JOSS Review: Example Python script is missing properties

[Andrew-S-Rosen]

RE: openjournals/joss-reviews#3089

In the main README, the example Python code crashes at isosurface.properties_norms because the surface does not have face properties. I would suggest one of two options:

1. Remove isosurface.properties_norms and isosurface.scalar_projection((0, 0, 1) to exclude the property mapping altogether or
2. Add property (e.g. velocity) data prior to calculating the norm of the vectors. A modified script is below that should work.

from pymatgen.io.vasp.outputs import Vasprun
from ifermi.surface import FermiSurface
from ifermi.interpolate import FourierInterpolator
from ifermi.plot import FermiSlicePlotter, FermiSurfacePlotter, save_plot, show_plot
from ifermi.kpoints import kpoints_from_bandstructure

# load VASP calculation outputs
vr = Vasprun("vasprun.xml")
bs = vr.get_band_structure()

# interpolate the energies onto a dense k-point mesh
interpolator = FourierInterpolator(bs)
dense_bs, velocities = interpolator.interpolate_bands(return_velocities=True)
dense_kpoints = kpoints_from_bandstructure(dense_bs)

# generate the Fermi surface and calculate the dimensionality
fs = FermiSurface.from_band_structure(
  dense_bs, mu=0.0, wigner_seitz=True, calculate_dimensionality=True,
  property_data=velocities, property_kpoints=dense_kpoints
)

# number of isosurfaces in the Fermi surface
fs.n_surfaces

# number of isosurfaces for each Spin channel
fs.n_surfaces_per_spin

# the total area of the Fermi surface
fs.area

# the area of each isosurface
fs.area_surfaces

# loop over all isosurfaces and check their properties
# the isosurfaces are given as a list for each spin channel
for spin, isosurfaces in fs.isosurfaces.items():
  for isosurface in isosurfaces:
    # the dimensionality (does the surface cross periodic boundaries)
    isosurface.dimensionality

    # what is the orientation
    isosurface.orientation

    # does the surface have face properties
    isosurface.has_properties

    # calculate the norms of the properties
    isosurface.properties_norms

    # calculate scalar projection of properties on to [0 0 1] vector
    isosurface.scalar_projection((0, 0, 1))

    # uniformly sample the surface faces to a consistent density
    isosurface.sample_uniform(0.1)

# plot the Fermi surface
fs_plotter = FermiSurfacePlotter(fs)
plot = fs_plotter.get_plot()

# generate Fermi slice along the (0 0 1) plane going through the Γ-point.
fermi_slice = fs.get_fermi_slice((0, 0, 1))

# number of isolines in the slice
fermi_slice.n_lines

# do the lines have segment properties
fermi_slice.has_properties

# plot slice
slice_plotter = FermiSlicePlotter(fermi_slice)
plot = slice_plotter.get_plot()

save_plot(plot, "fermi-slice.png")  # saves the plot to a file
show_plot(plot)  # displays an interactive plot

[utf]

Thanks @arosen93. This is a great catch. I will update the script to include the projections.

[utf]

Ok, the README has been updated.