Description:

To ensure seamless future integration between dreid-forge (parameterization) and dreid-kernel (evaluation), all potential energy parameter structures must be standardized to match the kernel's mathematical conventions.

The kernel uses half-force constants (k_half, v_half, c_half) to eliminate redundant multiplications during SIMD-optimized evaluation. Additionally, several potentials store pre-computed values (e.g., cos0 instead of theta0, r0_sq instead of r0) to minimize runtime operations. Current dreid-forge definitions diverge from these conventions, requiring a systematic refactoring.

Critical: The Inversion potential uses fundamentally different physics — kernel implements $E \propto \cos^2\psi$ while forge uses $E \propto (\chi - \chi_0)^2$. This must be corrected.

Tasks:

• Phase 1: Topology Structure Refactoring (src/model/topology.rs)

  • BondPotential::Harmonic: k_force → k_half (store $K/2$).
  • BondPotential::Morse: d0 → de (naming consistency).
  • AnglePotential::CosineHarmonic: (k_force, theta0) → (k_half, cos0).
  • AnglePotential::ThetaHarmonic: k_force → k_half.
  • DihedralPotential: (v_barrier, phase_offset) → (v_half, cos_n_phi0, sin_n_phi0).
  • ImproperPotential: Change formula from $(\chi-\chi_0)^2$ to $\cos^2\psi$ based, use c_half.
  • VdwPairPotential::LennardJones: (sigma, epsilon) → (d0, r0_sq).
  • VdwPairPotential::Exponential6: Add r_fusion_sq field.
  • HBondPotential: r0 → r_hb_sq, add cos_power: u8.

• Phase 2: Parameter Generation (src/forge/paramgen.rs)

  • Update generate_bond_potentials() to compute k_half = K/2.
  • Update generate_angle_potentials() to pre-compute cos0 = cos(θ₀).
  • Update generate_dihedral_potentials() to pre-compute (cos_n_φ₀, sin_n_φ₀).
  • Rewrite generate_improper_potentials() for cosine-based formula.
  • Update generate_vdw_potentials() to store squared distances.
  • Update generate_hbond_potentials() to store r_hb_sq and cos_power.

• Phase 3: IO & Test Updates

  • Update BGF writer to reverse transformations for output compatibility.
  • Update all unit tests for new parameter semantics.
  • Add cross-validation tests against dreid-kernel expected values.