PDOS: collinear spin support, atom sync, and BC parsing fix

[qihao-cheng]

Extend the SPARC PDOS post-processing utility (utils/pdos) to collinear spin-polarized calculations (SPIN_TYP = 1), keep the existing spin-unpolarized path, sync utils/atom with the latest SPARC-atomSFE sources (and adapt the PDOS Default path to that API), and harden BC parsing for filenames that contain substrings like BCC.

Summary

1. Collinear spin PDOS
   Read SPIN_TYP from the SPARC .out file (0 → unpolarized, 1 → collinear). Parse spin-resolved eigenvalues from .eigen and orbitals from .psi (SPARC write order: k-point → band → spin). Project each spin channel with spin degeneracy factor 1 (unpolarized path still uses 2). Noncollinear spin is not supported.

2. Spin-resolved outputs
   For collinear runs, write DOS_up.txt / DOS_down.txt, PDOS_up.txt / PDOS_down.txt, and a combined DOS.txt with columns Energy, DOS_up, DOS_down, DOS_tot (DOS_tot = up + down). Unpolarized runs still write DOS.txt / PDOS.txt as before.

3. Examples
   Add examples/Si2_nmag (SPIN_TYP: 0) and examples/Si2_nmag_spin (SPIN_TYP: 1, zero initial magnetization). On this closed-shell setup, net magnetization stays ~0 and the spectra can be compared after aligning to each Fermi level.

4. BC parsing fix
   Match the input tag BC: explicitly when reading the SPARC .out, so strings such as BCC in filenames are not treated as the boundary-condition line.

5. utils/atom sync + PDOS Default path
   Refresh the in-tree atomic DFT package from SPARC-atomSFE (data/, xc/ml_xc/, HF, response helpers, etc.), add a trimmed README/logo under utils/atom, and update PDOS’s Default atomic-orbital generator for the new solver API (verbose, solve(evaluate_basis_on_uniform_grid=True), n_l_orbitals shape (n_states, 2)).

6. Docs / versioning
   Update utils/pdos/README.md, ChangeLog, and the SPARC version banner in src/initialization.c to August 06, 2026.