CrystOD example directories (packaged copy)

These are the worked examples of CrystOD, installed with the package so that
they are available without cloning the repository.  Do not run them here:
their commands write output files next to the inputs.  Copy them into a
working directory first:

  crystod-example                  list the packaged examples
  crystod-example NN [NN ...]      copy examples (number or name) into ./example
  crystod-example NN -o DIR        copy into DIR instead
  crystod-example --all -o DIR     copy every packaged example into DIR

then cd into DIR/NN_name and follow its README.  The shared directories
test_POSCARs/ and test_XYZs/ are copied along with every example, and an
example that reads files of other examples brings those along, so the relative
paths in the READMEs (../test_POSCARs/..., ../NN_name/...) work in the copy.

Every file in the example and shared directories listed below is a
byte-for-byte copy of the same path under example/ of the CrystOD source tree;
only this README and index.json are generated (by
script/sync_packaged_examples.py).  Some data of example/ is not in the pip
package: large data (force-constant files, full MD trajectories), generated
HTML and PDF output, the reference data of the test suite, and the data of
work not yet published (unpublished, not distributed).  It stays in the
CrystOD development tree; the test suite and development need a clone of the
repository.

Examples
--------
01_wigner_d                  Wigner D matrices on real spherical harmonics (library API)
02_salc                      crystod (SALC: crystal-orbital irreps, hybridization)
03_hybridization             crystod (--atomic-orbital hybridization; --diagram crystal-orbital diagrams)
04_selection_rules           crystod --diagram (dipole selection rules of the crystal-orbital diagrams)
05_star_of_k                 crystod --star-of-k
06_visualized_basis          crystod --visualize (SALC viewer HTML)
08_direct_product            crystod-group --product / --table (point- and space-group irreps)
09_symmetric_square          crystod-group --product --symmetric / --antisymmetric, --jahn-teller
10_decompose_irrep           crystod-group --decompose
11_ligand_field_split        crystod-group --ligand-field
12_basis_function            crystod-group --basis
13_tensor_form               crystod-group --tensor (property-tensor forms)
14_generate_basis_function   crystod-group --generate-basis
15_show_coset                crystod-group --coset
16_correlate                 crystod-group --correlate (correlation and compatibility of irreps)
17_isotropy_subgroup         crystod-group --parent (isotropy subgroups)
18_invariants                crystod-group --parent --irrep --invariants (invariant polynomials)
19_child_lookup              crystod-group --parent G --child H (reverse lookup)
20_subgroup_graph            crystod-group --parent --irrep --graph (group-subgroup graph)
21_multiplet                 crystod-group --multiplet (spin multiplicities of irrep-shell configurations)
22_poscar2cif                crystod-group --poscar2cif / --cif2poscar (POSCAR <-> Bilbao-style CIF)
23_symmetry_mode             crystod-group --supergroup-cif (AMPLIMODES-style symmetry-mode analysis)
25_brillouin_zone            crystod-bz
26_bz_supercell              crystod-bz --trans-mat
28_phonon_irrep              crystod-phonon --irreps
29_phonon_activity           crystod-phonon --irreps / --vibration (IR / Raman / silent / acoustic activity at Gamma)
30_phonon_fatband            crystod-phonon --fatband
31_phonon_lt                 crystod-phonon --lt
32_phonon_vector             crystod-phonon --vector
33_modulation                crystod-phonon --modulation
34_vibration                 crystod-phonon --vibration
36_spin_basis                crystod-mag
37_magnetic_group            crystod-mag --classify-only (magnetic space groups, altermagnet classes)
39_xdatcar2adp               crystod-md --adp (and --summary on the same XDATCAR)
40_md_projection             crystod-md --project (mode projection of an MD trajectory)
42_molecular_salc            crystod-mol (--symmetry and molecular SALCs)
43_molod                     crystod-mol --diagram (MO diagrams: symmetry + overlap, or --pyscf)
45_python_api                the library API (crystod.phonon etc.) on the SrTiO3 data
46_xrd_pattern               crystod-xrd (powder X-ray diffraction patterns)
47_xrd_superlattice          crystod-xrd --parent / --radiation neutron (superlattice reflections, k points, irreps)
48_mp_search                 crystod-search (Materials Project search and POSCAR download; needs an API key)

Examples that read files of other examples (copied together):
  29_phonon_activity   28_phonon_irrep 30_phonon_fatband
  40_md_projection     33_modulation 39_xdatcar2adp
  45_python_api        28_phonon_irrep
  47_xrd_superlattice  23_symmetry_mode

Shared directories
------------------
test_POSCARs                 shared input structures used by the examples and testsuite
test_XYZs                    shared molecule files (O2, H2O, NH3, CH4, SF6) for crystod-mol
