Fix #8078: Refactor: remove the UnitCell Statistics layer and flattening reference members

[mohanchen]

Fix #8078

Motivation

UnitCell stored its atom-count and index-map data in a nested Statistics st struct and re-exported every field as a reference member bound at
construction (int& nat = st.nat, int*& iat2it = st.iat2it, ...). This
design caused several concrete problems:

1. Dual-view aliasing — every field is reachable under two names
   (ucell.nat and ucell.st.nat), both used interchangeably across the
   codebase, making the data flow hard to follow and grep-based refactoring
   unreliable.
2. An invisible ownership rule — the four index arrays (iat2it,
   iat2ia, iwt2iat, iwt2iw) were raw int* owned by Statistics,
   whose destructor delete[]d them. Test fixtures had to new[] them but
   never delete[] them, a rule that was only documented in AGENTS.md;
   several unit tests double-freed as a result.
3. A latent shallow-copy double-free — the reference members silently
   deleted the implicit copy assignment while leaving the implicit copy
   constructor available; that constructor shallow-copies the owning int*
   members, so copying a UnitCell would double-free.

Changes

• Repoint the only consumers of the Statistics type. The
  symmetry-related modules (source_cell/module_symmetry/* and
  source_lcao/module_ri/module_exx_symmetry/*) previously took
  const Statistics& in ~20 function signatures; they now take
  const UnitCell& (forward-declared where the header only declares).
  All call sites pass ucell (or *ucell where ucell is a pointer).
• Move the nine fields into UnitCell as direct members under the
  existing top-level names, so the many ucell.nat-style call sites are
  unchanged. The st member, the nine reference members, and the
  Statistics struct are deleted.
• Convert iat2it/iat2ia/iwt2iat/iwt2iw from raw int* to
  std::vector<int>. The ~100 allocation sites (production:
  unitcell.cpp, cal_wfc.cpp; the rest in test fixtures) migrate from
  new int[]/delete[] to resize()/assign(). The two device-upload
  call sites in force_pw.cpp now use .data(). Element access X[i] is
  unchanged everywhere.
• Delete UnitCell copy constructor/assignment and default the move
  operations, so accidental copies fail at compile time instead of
  double-freeing at runtime. No existing code copies a UnitCell
  (verified by grep), so this changes no behavior.
• Update AGENTS.md: replace the obsolete fixture note ("do not
  delete[] iat2it") with the new ownership/vector rule.

Scope / non-goals

• The Lattice lat block follows the same flattening-reference pattern but
  is intentionally out of scope. Unlike Statistics, Lattice is a
  genuinely cohesive type passed by value/reference to many consumers
  (bcast_Lattice, remake_cell, update_pos_tau, analy_sys,
  pyabacus), so the struct should be kept; only its reference aliases need
  removal. That is a larger, independent change left for a follow-up PR.
• No INPUT parameter or user-facing behavior change.

Verification

• Full build succeeds with no compile errors.
• OMP_NUM_THREADS=1 ctest -R "unitcell|CELL_SYMMETRY|symmetry|hcontainer| dftu|operator_lcao|module_dm|pdos|hsr|restart_exx|gint|relax|esolver":
  33/33 passed. (Full ctest is not runnable in this sandbox — GPU
  device tests and tests that write to absolute paths fail with
  process_reader/code=11 environment noise; the related-test subset is
  green.)
• tools/03_code_analysis/agent_governance_check.py --base HEAD~1 --head HEAD:
  4 warnings, all benign and explained below; no blockers.
  • irreducible_sector.h:99-100 "new default parameters" — false positive:
    the default arguments pre-date this change; the lines only appear in the
    diff because the parameter was renamed st → ucell.
  • unitcell.h adds <vector> — required: the new members are value-type
    std::vector<int> and need the complete type.
  • symm_rotation.h adds unitcell.h — required: the header directly
    includes two .hpp implementation files whose inline templates
    dereference ucell.iat2it, so it must hold the complete type.
  • "docs sync review" — no INPUT/user-facing change, so
    docs/parameters.yaml and docs/advanced/input_files/input-main.md are
    intentionally untouched.
• Final greps: no Statistics, no ucell.st / ->st (in the UnitCell
  sense), no remaining new int[] / delete[] for the four index arrays.

Notes for reviewers

• The large file count is almost entirely the mechanical
  new int[] → resize() migration in test fixtures; each per-file diff is
  small.
• One non-mechanical change worth a look:
  source_lcao/module_dftu/unittests/test_dftu_nao_ijr.cpp previously bound
  the index arrays to fixture-owned buffer vectors via raw pointers
  (ucell.iat2it = iat2it_buf.data()) and reset them to nullptr in
  TearDown — a workaround for the old pointer-ownership model. Now that the
  members are vectors, it uses assign()/resize() directly and the buffer
  members and reset logic are removed. Semantically equivalent and simpler.