def __str__(self):
elem = f"{self.element:>4}"
dist = f"{self.distance:4.2f}"
ini_coords = pretty_coords(self.initial_coords)
p_coords = pretty_coords(self.perturbed_coords)
disp = f"{self.displacement:7.2f}"
return f"{elem} {dist} {ini_coords} -> {p_coords} {disp}"
def __str__(self):
sym_transition = f"{self.initial_site_sym} " \
f"-> {self.final_site_sym} ({self.symm_relation})"
center_coords = pretty_coords(self.center)
lines = [
" -- defect structure info", f"Defect type: {self.defect_type}",
f"Site symmetry: {sym_transition}",
f"Has same configuration from initial structure: "
f"{self.same_config_from_init}",
f"Drift distance: {self.drift_dist:5.3f}",
f"Defect center: {center_coords}"
]
def _site_info(header: str, site_info: List[SiteInfo]):
if not site_info:
return []
_table = tabulate([[idx, elem, pretty_coords(coords)]
for idx, elem, coords in site_info],
tablefmt="plain")
return [header, _table, ""]
lines.extend(_site_info("Removed atoms:", self.site_diff.removed))
lines.extend(_site_info("Added atoms:", self.site_diff.inserted))
if self.same_config_from_init is False:
lines.extend(
_site_info("Removed atoms from initial structure:",
self.site_diff_from_initial.removed))
lines.extend(
_site_info("Inserted atoms to initial structure:",
self.site_diff_from_initial.inserted))
lines.append("Displacements")
idxs = [[i, d] for i, d in enumerate(self.displacements)
if d is not None]
table = [[
"Elem", "Dist", "Displace", "Angle", "Index", "Initial site", "",
"Final site"
]]
for final_idx, d in sorted(idxs,
key=lambda y: y[1].distance_from_defect):
if d.distance_from_defect > defaults.show_structure_cutoff:
break
i_pos = pretty_coords(d.original_pos)
f_pos = pretty_coords(d.final_pos)
angle = int(round(d.angle, -1)) if d.angle else ""
table.append([
d.specie,
round(d.distance_from_defect, 2),
round(d.displace_distance, 2), angle, final_idx, i_pos, "->",
f_pos
])
lines.append(tabulate(table, tablefmt="plain"))
return "\n".join(lines)
def show_edge_info(edge_info: EdgeInfo):
return [
edge_info.band_idx, edge_info.energy,
f"{edge_info.occupation:5.2f}",
pretty_orbital(edge_info.orbital_info.orbitals),
pretty_coords(edge_info.kpt_coord)
]
def _site_info(header: str, site_info: List[SiteInfo]):
if not site_info:
return []
_table = tabulate([[idx, elem, pretty_coords(coords)]
for idx, elem, coords in site_info],
tablefmt="plain")
return [header, _table, ""]
def _kpt_block(self):
kpt_block = [["Index", "Coords", "Weight"]]
for index, (kpt_coord, kpt_weight) in enumerate(
zip(self.kpt_coords, self.kpt_weights), 1):
coord = pretty_coords(kpt_coord)
weight = f"{kpt_weight:4.3f}"
kpt_block.append([index, coord, weight])
return tabulate(kpt_block, tablefmt="plain")
def _show_edge_info(edge_info: EdgeInfo, orb_diff: float):
return [
edge_info.band_idx + 1, f"{edge_info.energy:7.3f}",
f"{edge_info.p_ratio:5.2f}", f"{edge_info.occupation:5.2f}",
f"{orb_diff:5.2f}",
pretty_orbital(edge_info.orbital_info.orbitals),
pretty_coords(edge_info.kpt_coord)
]
def _add_band_info(self, band_idx, c_dist, lines, spin):
try:
radius = f"{self.half_charge_radius(band_idx, spin):6.3f}"
except ValueError:
radius = "None"
spin_idx = 0 if spin == Spin.up else 1
spin_str = "up" if spin == Spin.up else "down"
center = pretty_coords(c_dist[spin_idx].charge_center)
lines.append([band_idx + 1, spin_str, radius, center])
def __str__(self):
min_or_max = "min" if self.is_min else "max"
extrema_points = [[
"#", "site_sym", "coordination", "frac_coords", "quantity"
]]
for idx, ep in enumerate(self.extrema_points, 1):
extrema_points.append([
idx, ep.site_symmetry, ep.coordination.distance_dict,
pretty_coords(ep.frac_coords[0]), f"{ep.quantities[0]:.2g}"
])
lines = [
f"info: {self.info}", f"min_or_max: {min_or_max}",
f"extrema_points:",
tabulate(extrema_points, tablefmt="plain")
]
return "\n".join(lines)
def _orbital_info(self):
inner_table = [[
"Index", "Energy", "P-ratio", "Occupation", "Orbitals"
]]
w_radius = self.localized_orbitals and self.localized_orbitals[0].radius
if w_radius:
inner_table[0].extend(["Radius", "Center"])
for lo in self.localized_orbitals:
participation_ratio = f"{lo.participation_ratio:5.2f}" \
if lo.participation_ratio else "None"
inner = [
lo.band_idx + 1, f"{lo.ave_energy:7.3f}", participation_ratio,
f"{lo.occupation:5.2f}",
pretty_orbital(lo.orbitals)
]
if w_radius:
inner.extend([f"{lo.radius:5.2f}", pretty_coords(lo.center)])
inner_table.append(inner)
return tabulate(inner_table, tablefmt="plain")
def test_pretty_coords():
assert pretty_coords([0.1, 0.2, 0.3]) == "( 0.100, 0.200, 0.300)"
assert pretty_coords([1, -2, 0]) == "( 1.000, -2.000, 0.000)"