[Code scan] Fix VASP tutorial commands and parsed output paths

[njzjz]

This issue comes from a Codex global repository scan.

Problem

The VASP quickstart points --root at a single calculation directory and uses an empty prefix:

dftio/docs/user-guide/quickstart.md

Lines 21 to 28 in c9d128f

	```bash
	dftio parse \
	--mode vasp \
	--root example/vasp/GaAs \
	--prefix "" \
	--outroot ./parsed_data \
	--eigenvalue
	```

The parser discovers calculations with glob(os.path.join(root, '*' + prefix + '*')):

dftio/dftio/io/parse.py

Lines 64 to 67 in c9d128f

	if isinstance(root, list) and all(isinstance(item, str) for item in root):
	self.raw_datas = root
	else:
	self.raw_datas = glob.glob(os.path.join(root, '*' + prefix + '*'))

With --root example/vasp/GaAs --prefix "", discovery returns files like EIGENVAL and POSCAR, then the VASP parser tries to read EIGENVAL/POSCAR:

dftio/dftio/io/vasp/vasp_parser.py

Lines 25 to 28 in c9d128f

	super(VASPParser, self).__init__(root, prefix)
	self.raw_sys = [read(self.raw_datas[idx]+'/POSCAR') for idx in range(len(self.raw_datas))]
	log.warning("VASP parser only supports the static (SCF or NSCF) calculations. MD and RELAX is not supported yet.")

The band tutorial has the same root issue and also omits --eigenvalue:

dftio/docs/tutorials/plot_bands.md

Lines 16 to 21 in c9d128f

	```bash
	dftio parse \
	--mode vasp \
	--root example/vasp/GaAs \
	--outroot ./parsed_bands
	```

The docs also describe a top-level 0.dat, but write_dat() creates <formula>.<idx>/cell.dat, kpoints.npy, and eigenvalues.npy:

dftio/dftio/io/parse.py

Lines 251 to 267 in c9d128f

	out_dir = os.path.join(outroot, self.formula(idx=idx)+".{}".format(idx))
	os.makedirs(out_dir, exist_ok=True)
	# The abacus must have PBC, so here we save cell by default
	# np.savetxt(os.path.join(out_dir, "cell.dat"), structure[_keys.CELL_KEY].reshape(-1, 3))
	# np.savetxt(os.path.join(out_dir, "positions.dat"), structure[_keys.POSITIONS_KEY].reshape(-1, 3))
	# np.savetxt(os.path.join(out_dir, "atomic_numbers.dat"), structure[_keys.ATOMIC_NUMBERS_KEY], fmt='%d')
	# np.savetxt(os.path.join(out_dir, "pbc.dat"), structure[_keys.PBC_KEY])
	# write structure
	self.write_struct(structure, out_dir, fmt=fmt)
	# write eigenvalue
	if eigenvalue:
	eigstatus = self.get_eigenvalue(idx=idx, band_index_min=band_index_min)
	self.check_eigenvalue(idx=idx, eigstatus=eigstatus)
	np.save(os.path.join(out_dir, "kpoints.npy"), eigstatus[_keys.KPOINT_KEY])
	np.save(os.path.join(out_dir, "eigenvalues.npy"), eigstatus[_keys.ENERGY_EIGENVALUE_KEY])

dftio band -r ./parsed_data points one directory too high, and the plot file is band_structure.png:

dftio/dftio/plot/plot_eigs.py

Lines 60 to 91 in c9d128f

	self.kpoints = np.load(os.path.join(self.path, "kpoints.npy"))
	self.eigs = np.load(os.path.join(self.path, "eigenvalues.npy"))
	if len(self.eigs.shape)==3 :
	assert self.eigs.shape[0]== 1, "only 1 band structure is supported!"
	self.eigs = self.eigs[0]
	assert self.eigs.shape[0] == self.kpoints.shape[0], "eigenvalues and kpoints shape mismatch!"
	def plot(self, bmin:int=0, bmax:int=None):
	# plot band structure
	fig, ax = plt.subplots()
	nbands = self.eigs.shape[1]
	if bmax is None:
	bmax = nbands
	else:
	bmax = min(bmax, nbands)
	assert bmax>bmin, "max should be larger than min!"
	if self.kpoints.shape[0] > 1:
	ax.plot(self.eigs[:,bmin:bmax], 'b-', lw=1)
	ax.set_xlabel("k-point")
	ax.set_title("Band Structure")
	else:
	for e in self.eigs[0, bmin:bmax]:
	ax.hlines(e, xmin=-0.5, xmax=0.5, color='b', linewidth=1)
	ax.set_xticks([])
	ax.set_title("Energy levels")
	ax.text(0.5, 0.5, f"band windown: {bmin} - {bmax}", ha='center', va='center', transform=ax.transAxes)
	ax.set_ylabel("Energy (eV)")
	plt.savefig(os.path.join(self.path, "band_structure.png"), dpi=300)

Suggested fix

Use a command like --root example/vasp --prefix GaAs --eigenvalue, document the generated <formula>.0 subdirectory, and point dftio band -r at that subdirectory. Update the expected plot filename to band_structure.png.