fix: [Phase 3] Implement Delocalization Index (DI)

[newtontech]

Summary

This PR implements the Delocalization Index (DI) for analyzing electron pair sharing and aromaticity in molecular systems. The implementation includes 2-center and 3-center DI calculations, aromaticity indices (AI, PDI, FLU), and bond classification based on DI values.

Changes

• pymultiwfn/bonding/delocalization.py: New module implementing:

  • delocalization_index(): 2-center DI calculation
  • three_center_delocalization_index(): 3-center DI for multi-center bonds
  • calculate_di_matrix(): Full DI matrix generation
  • classify_bond_from_di(): Bond type classification
  • calculate_aromaticity_index(): Ring aromaticity measure
  • calculate_pdi(): Para-Delocalization Index for 6-membered rings
  • calculate_flu(): Aromatic Fluctuation Index
  • DelocalizationIndex class: Main analysis interface

• pymultiwfn/bonding/init.py: Updated to export new DI classes and functions

• tests/bonding/test_delocalization_index.py: Comprehensive test suite with 35 passing tests covering:

  • Basic DI calculations
  • 3-center DI symmetry
  • DI matrix properties
  • Bond classification
  • Aromaticity indices
  • Class initialization and methods

Testing

All 35 tests pass:

• TestDelocalizationIndexFunction: 6 tests
• TestThreeCenterDI: 2 tests
• TestDIMatrix: 3 tests
• TestBondClassification: 6 tests
• TestAromaticityIndices: 6 tests
• TestDelocalizationIndexClass: 9 tests
• TestDelocalizationResult: 3 tests

API Example

from pymultiwfn.bonding import DelocalizationIndex

di = DelocalizationIndex(wfn)
di_val = di.get_delocalization_index(atom_i=0, atom_j=1)
print(f"DI: {di_val:.3f} e")

# For aromaticity analysis
ring_atoms = [0, 1, 2, 3, 4, 5]  # benzene ring
ai = di.get_aromaticity_index(ring_atoms)
pdi = di.get_pdi(ring_atoms)
flu = di.get_flu(ring_atoms)
print(f"Aromaticity Index: {ai:.3f}")
print(f"PDI: {pdi:.3f} e")
print(f"FLU: {flu:.3f}")

Fixes #4

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