MultiOptPy 1.20.4__py3-none-any.whl → 1.20.6__py3-none-any.whl

multioptpy/ModelHessian/fischerd3.py

@@ -1,360 +1,305 @@
 import numpy as np
-from scipy.spatial.distance import cdist # Highly recommended for vectorized distance calculation
+from scipy.spatial.distance import cdist
 from multioptpy.Parameters.parameter import UnitValueLib, covalent_radii_lib
 from multioptpy.Utils.calc_tools import Calculationtools
 from multioptpy.Parameters.parameter import D3Parameters, D2_C6_coeff_lib, D2_VDW_radii_lib
 from multioptpy.Utils.bond_connectivity import BondConnectivity
-from multioptpy.ModelHessian.calc_params import torsion2, stretch2, bend2
-
+from multioptpy.ModelHessian.calc_params import torsion2, bend2
 
 class FischerD3ApproxHessian:
     def __init__(self):
         """
-        Fischer's Model Hessian implementation with D3 dispersion correction
-        Ref: Fischer and Almlöf, J. Phys. Chem., 1992, 96, 24, 9768–9774
-        Implementation Ref.: pysisyphus.optimizers.guess_hessians
+        Fischer's Model Hessian implementation with Dynamic D3 dispersion correction.
+        Robust against linear molecules and singularities.
         """
         self.bohr2angstroms = UnitValueLib().bohr2angstroms
-        self.hartree2kcalmol = UnitValueLib().hartree2kcalmol
-        self.bond_factor = 1.3  # Bond detection threshold factor
         
-        # D3 dispersion correction parameters (default: PBE0)
+        # D3 dispersion correction parameters
         self.d3_params = D3Parameters()
         self.cart_hess = None
         
+        # Grimme D3 scaling factors for CN calculation
+        self.k1 = 16.0
+        self.k2 = 4.0 / 3.0
+
+        # Expanded Reference Coordination Numbers (Default averages)
+        # Covers H through Xe roughly. Values are heuristic/typical valencies or coordination.
+        self.ref_cn_map = {
+            # Period 1
+            'H': 1, 'He': 0,
+            # Period 2
+            'Li': 4, 'Be': 4, 'B': 3, 'C': 4, 'N': 3, 'O': 2, 'F': 1, 'Ne': 0,
+            # Period 3
+            'Na': 6, 'Mg': 6, 'Al': 6, 'Si': 4, 'P': 5, 'S': 6, 'Cl': 1, 'Ar': 0,
+            # Period 4 (Transition Metals set to ~6-12 depending on typical packing/complexes)
+            'K': 8, 'Ca': 6, 
+            'Sc': 12, 'Ti': 12, 'V': 12, 'Cr': 6, 'Mn': 6, 'Fe': 6, 'Co': 6, 'Ni': 4, 'Cu': 4, 'Zn': 4,
+            'Ga': 4, 'Ge': 4, 'As': 3, 'Se': 2, 'Br': 1, 'Kr': 0,
+            # Period 5
+            'Rb': 8, 'Sr': 6,
+            'Y': 12, 'Zr': 12, 'Nb': 12, 'Mo': 6, 'Tc': 6, 'Ru': 6, 'Rh': 6, 'Pd': 4, 'Ag': 4, 'Cd': 4,
+            'In': 6, 'Sn': 4, 'Sb': 3, 'Te': 2, 'I': 1, 'Xe': 0
+        }
+
+    def calc_coordination_numbers(self, coord, element_list):
+        """Calculate fractional coordination numbers (CN) for Dynamic D3."""
+        # Pre-fetch covalent radii
+        cov_r = np.array([covalent_radii_lib(e) for e in element_list])
+        
+        # Vectorized distance matrix
+        r_mat = cdist(coord, coord)
+        np.fill_diagonal(r_mat, np.inf)
+        
+        # rcov_sum[i, j] = cov_r[i] + cov_r[j]
+        rcov_sum = cov_r[:, None] + cov_r[None, :]
+        
+        # D3 CN formula
+        term = -self.k1 * (self.k2 * (r_mat / rcov_sum) - 1.0)
+        term = np.clip(term, -100, 100) # Prevent overflow
+        cutoff_func = 1.0 / (1.0 + np.exp(term))
+        
+        return np.sum(cutoff_func, axis=1)
+
+    # --- Fischer Terms (Robust) ---
+
     def calc_bond_force_const(self, r_ab, r_ab_cov):
-        """Calculate force constant for bond stretching using Fischer formula"""
         return 0.3601 * np.exp(-1.944 * (r_ab - r_ab_cov))
         
     def calc_bend_force_const(self, r_ab, r_ac, r_ab_cov, r_ac_cov):
-        """Calculate force constant for angle bending"""
         val = r_ab_cov * r_ac_cov
-        if abs(val) < 1.0e-10:
-            return 0.0
-        
-        return 0.089 + 0.11 / (val) ** (-0.42) * np.exp(
-            -0.44 * (r_ab + r_ac - r_ab_cov - r_ac_cov)
-        )
+        if abs(val) < 1e-10: return 0.0
+        return 0.089 + 0.11 / (val)**(-0.42) * np.exp(-0.44 * (r_ab + r_ac - r_ab_cov - r_ac_cov))
         
     def calc_dihedral_force_const(self, r_ab, r_ab_cov, bond_sum):
-        """Calculate force constant for dihedral torsion"""
         val = r_ab * r_ab_cov
-        if abs(val) < 1.0e-10:
-            return 0.0
-        return 0.0015 + 14.0 * max(bond_sum, 0) ** 0.57 / (val) ** 4.0 * np.exp(
-            -2.85 * (r_ab - r_ab_cov)
-        )
-    
-    def get_c6_coefficient(self, element_i, element_j):
-        """Get C6 coefficient based on D3 model (simplified)"""
-        c6_i = D2_C6_coeff_lib(element_i)
-        c6_j = D2_C6_coeff_lib(element_j)
-        c6_ij = np.sqrt(c6_i * c6_j)
-        return c6_ij
-    
-    def get_c8_coefficient(self, element_i, element_j):
-        """Calculate C8 coefficient based on D3 model using reference r4r2 values"""
-        c6_ij = self.get_c6_coefficient(element_i, element_j)
-        r4r2_i = self.d3_params.get_r4r2(element_i)
-        r4r2_j = self.d3_params.get_r4r2(element_j)
-        c8_ij = 3.0 * c6_ij * np.sqrt(r4r2_i * r4r2_j)
-        return c8_ij
-    
-    def get_r0_value(self, element_i, element_j):
-        """Calculate R0 value for D3 model (characteristic distance for atom pair)"""
-        try:
-            r_i = D2_VDW_radii_lib(element_i)
-            r_j = D2_VDW_radii_lib(element_j)
-            return r_i + r_j
-        except:
-            r_i = covalent_radii_lib(element_i) * 1.5
-            r_j = covalent_radii_lib(element_j) * 1.5
-            return r_i + r_j
-    
-    def d3_damping_function(self, r_ij, r0, order=6):
-        """BJ (Becke-Johnson) damping function for D3"""
-        if order == 6:
-            a1, a2 = self.d3_params.a1, self.d3_params.a2
-        else:
-            a1, a2 = self.d3_params.a1, self.d3_params.a2 + 2.0
-            
-        denominator = r_ij**order + (a1 * r0 + a2)**order
-        return r_ij**order / denominator
+        if abs(val) < 1e-10: return 0.0
+        return 0.0015 + 14.0 * max(bond_sum, 0)**0.57 / (val)**4.0 * np.exp(-2.85 * (r_ab - r_ab_cov))
 
-    def d3_hessian_contribution(self, r_vec, r_ij, element_i, element_j):
-        """Calculate D3 dispersion contribution to Hessian"""
-        if r_ij < 0.1:
-            return np.zeros((3, 3))
-            
-        c6_ij = self.get_c6_coefficient(element_i, element_j)
-        c8_ij = self.get_c8_coefficient(element_i, element_j)
-        r0 = self.get_r0_value(element_i, element_j)
-        
-        f_damp6 = self.d3_damping_function(r_ij, r0, order=6)
-        f_damp8 = self.d3_damping_function(r_ij, r0, order=8)
-        
-        # Derivatives of damping functions
-        a1, a2 = self.d3_params.a1, self.d3_params.a2
-        a1_8, a2_8 = self.d3_params.a1, self.d3_params.a2 + 2.0
-        
-        denom6 = r_ij**6 + (a1 * r0 + a2)**6
-        denom8 = r_ij**8 + (a1_8 * r0 + a2_8)**8
-        
-        # df_damp/dr
-        df_damp6 = 6 * r_ij**5 / denom6 - 6 * r_ij**12 / denom6**2
-        df_damp8 = 8 * r_ij**7 / denom8 - 8 * r_ij**16 / denom8**2
-        
-        # dE/dr (Gradient magnitude)
-        g6 = -self.d3_params.s6 * c6_ij * ((-6.0 / r_ij**7) * f_damp6 + (1.0 / r_ij**6) * df_damp6)
-        g8 = -self.d3_params.s8 * c8_ij * ((-8.0 / r_ij**9) * f_damp8 + (1.0 / r_ij**8) * df_damp8)
-        
-        # Unit vector and projection operator
-        unit_vec = r_vec / r_ij
-        proj_op = np.outer(unit_vec, unit_vec) # P = r_hat * r_hat^T
-        
-        # Coefficients for H = (d^2E/dr^2) * P + (1/r * dE/dr) * (I - P)
-        # Using the simplified structure from the original code for d^2E/dr^2 approximation:
-        h6_proj_coeff = self.d3_params.s6 * c6_ij / r_ij**8 * (42.0 * f_damp6 - r_ij * df_damp6)
-        h8_proj_coeff = self.d3_params.s8 * c8_ij / r_ij**10 * (72.0 * f_damp8 - r_ij * df_damp8)
-        
-        h_proj = h6_proj_coeff + h8_proj_coeff # d^2E/dr^2 approximation
-        h_perp = (g6 + g8) / r_ij             # 1/r * dE/dr (Perpendicular coefficient)
-        
-        # Construct Hessian matrix
-        identity = np.eye(3)
-        hessian = h_proj * proj_op + h_perp * (identity - proj_op)
-        
-        return hessian
+    def _add_block(self, i, j, block):
+        start_i, end_i = 3*i, 3*i+3
+        start_j, end_j = 3*j, 3*j+3
+        self.cart_hess[start_i:end_i, start_j:end_j] += block
 
-    # --- Optimized: Vectorized connectivity calculation ---
-    def get_bond_connectivity(self, coord, element_list):
-        """Calculate bond connectivity matrix and related data (Optimized with vectorization)"""
-        n_atoms = len(coord)
-        
-        # 1. Distance matrix (Vectorized)
-        try:
-            dist_mat = cdist(coord, coord)
-        except NameError:
-            diff = coord[:, None, :] - coord[None, :, :]
-            dist_mat = np.linalg.norm(diff, axis=-1)
-
-        # 2. Covalent radii sums (Vectorized)
-        cov_radii = np.array([covalent_radii_lib(e) for e in element_list])
-        pair_cov_radii_mat = cov_radii[:, None] + cov_radii[None, :]
-        
-        # 3. Bond connectivity matrix
-        bond_mat = dist_mat <= (pair_cov_radii_mat * self.bond_factor)
-        np.fill_diagonal(bond_mat, False)
-        
-        return bond_mat, dist_mat, pair_cov_radii_mat
-    
-    # --- Optimized: Block assignment using slicing ---
-    def fischer_bond(self, coord, element_list):
-        """Calculate Hessian components for bond stretching (Optimized with slicing)"""
-        BC = BondConnectivity()
-        b_c_mat = BC.bond_connect_matrix(element_list, coord)
-        bond_indices = BC.bond_connect_table(b_c_mat)
-        
+    def fischer_bond(self, coord, element_list, bond_indices):
         for idx in bond_indices:
             i, j = idx
-            r_ij = np.linalg.norm(coord[i] - coord[j])
-            r_ij_cov = covalent_radii_lib(element_list[i]) + covalent_radii_lib(element_list[j])
-            
-            force_const = self.calc_bond_force_const(r_ij, r_ij_cov)
-            
-            t_xyz = np.array([coord[i], coord[j]])
-            r, b_vec = stretch2(t_xyz)
+            r_vec = coord[i] - coord[j]
+            r_ij = np.linalg.norm(r_vec)
+            if r_ij < 0.1: continue
+
+            r_cov = covalent_radii_lib(element_list[i]) + covalent_radii_lib(element_list[j])
+            fc = self.calc_bond_force_const(r_ij, r_cov)
             
-            # Optimized: Use NumPy slicing and outer product
-            b_vec_i, b_vec_j = b_vec[0], b_vec[1] 
+            # Use safe unit vector calculation
+            u = r_vec / r_ij
+            block = fc * np.outer(u, u)
             
-            H_ii_block = force_const * np.outer(b_vec_i, b_vec_i)
-            H_jj_block = force_const * np.outer(b_vec_j, b_vec_j)
-            H_ij_block = force_const * np.outer(b_vec_i, b_vec_j)
-            H_ji_block = force_const * np.outer(b_vec_j, b_vec_i) 
-
-            start_i, end_i = 3 * i, 3 * i + 3
-            start_j, end_j = 3 * j, 3 * j + 3
-
-            self.cart_hess[start_i:end_i, start_i:end_i] += H_ii_block
-            self.cart_hess[start_j:end_j, start_j:end_j] += H_jj_block
-            self.cart_hess[start_i:end_i, start_j:end_j] += H_ij_block
-            self.cart_hess[start_j:end_j, start_i:end_i] += H_ji_block
-
+            self._add_block(i, i, block)
+            self._add_block(j, j, block)
+            self._add_block(i, j, -block)
+            self._add_block(j, i, -block)
 
-    def fischer_angle(self, coord, element_list):
-        """Calculate Hessian components for angle bending (Optimized with slicing)"""
-        BC = BondConnectivity()
-        b_c_mat = BC.bond_connect_matrix(element_list, coord)
-        angle_indices = BC.angle_connect_table(b_c_mat)
-        
+    def fischer_angle(self, coord, element_list, angle_indices):
         for idx in angle_indices:
-            i, j, k = idx  # i-j-k angle
-            r_ij = np.linalg.norm(coord[i] - coord[j])
-            r_jk = np.linalg.norm(coord[j] - coord[k])
-            r_ij_cov = covalent_radii_lib(element_list[i]) + covalent_radii_lib(element_list[j])
-            r_jk_cov = covalent_radii_lib(element_list[j]) + covalent_radii_lib(element_list[k])
+            i, j, k = idx
+            r_ij_vec = coord[i] - coord[j]
+            r_jk_vec = coord[k] - coord[j] # Center is j
             
-            force_const = self.calc_bend_force_const(r_ij, r_jk, r_ij_cov, r_jk_cov)
+            r_ij = np.linalg.norm(r_ij_vec)
+            r_jk = np.linalg.norm(r_jk_vec)
             
-            t_xyz = np.array([coord[i], coord[j], coord[k]])
-            theta, b_vec = bend2(t_xyz)
+            if r_ij < 0.1 or r_jk < 0.1: 
+                continue
+
+            # Check for linearity (180 deg) or overlap (0 deg)
+            cos_theta = np.dot(r_ij_vec, r_jk_vec) / (r_ij * r_jk)
+            if abs(cos_theta) > 0.9999:
+                 continue
+
+            r_cov_ij = covalent_radii_lib(element_list[i]) + covalent_radii_lib(element_list[j])
+            r_cov_jk = covalent_radii_lib(element_list[j]) + covalent_radii_lib(element_list[k])
             
-            # Optimized: Use NumPy slicing and outer product
-            atoms = [i, j, k]
+            fc = self.calc_bend_force_const(r_ij, r_jk, r_cov_ij, r_cov_jk)
             
-            for m_idx, m_atom in enumerate(atoms):
-                for n_idx, n_atom in enumerate(atoms):
-                    start_m, end_m = 3 * m_atom, 3 * m_atom + 3
-                    start_n, end_n = 3 * n_atom, 3 * n_atom + 3
-                    
-                    H_mn_block = force_const * np.outer(b_vec[m_idx], b_vec[n_idx])
-                    self.cart_hess[start_m:end_m, start_n:end_n] += H_mn_block
-
+            try:
+                # bend2 expects: [atom_end1, atom_center, atom_end2]
+                t_xyz = np.array([coord[i], coord[j], coord[k]])
+                _, b_vec = bend2(t_xyz)
+                
+                atoms = [i, j, k]
+                for m_idx, m_atom in enumerate(atoms):
+                    for n_idx, n_atom in enumerate(atoms):
+                        block = fc * np.outer(b_vec[m_idx], b_vec[n_idx])
+                        self._add_block(m_atom, n_atom, block)
+            except Exception:
+                continue
 
-    def fischer_dihedral(self, coord, element_list, bond_mat):
-        """Calculate Hessian components for dihedral torsion (Optimized with singularity damping)"""
-        BC = BondConnectivity()
-        b_c_mat = BC.bond_connect_matrix(element_list, coord)
-        dihedral_indices = BC.dihedral_angle_connect_table(b_c_mat)
-        
-        # Calculate bond count for central atoms in dihedrals
-        tors_atom_bonds = {}
-        for idx in dihedral_indices:
-            i, j, k, l = idx  # i-j-k-l dihedral
-            bond_sum = bond_mat[j].sum() + bond_mat[k].sum() - 2
-            tors_atom_bonds[(j, k)] = bond_sum
+    def fischer_dihedral(self, coord, element_list, dihedral_indices, bond_mat):
+        neighbor_counts = np.sum(bond_mat, axis=1)
 
         for idx in dihedral_indices:
             i, j, k, l = idx
             
-            # Vector calculations
+            # Check linearity of the axis bond j-k and its connections
             vec_ji = coord[i] - coord[j]
             vec_jk = coord[k] - coord[j]
             vec_kl = coord[l] - coord[k]
             
-            r_jk = np.linalg.norm(vec_jk)
-            r_jk_cov = covalent_radii_lib(element_list[j]) + covalent_radii_lib(element_list[k])
-            
-            bond_sum = tors_atom_bonds.get((j, k), 0)
-            
-            # Calculate base force constant
-            force_const = self.calc_dihedral_force_const(r_jk, r_jk_cov, bond_sum)
-            
-            # --- Singularity Handling (Damping for linear angles) ---
-            # Determine linearity of angles i-j-k and j-k-l
-            
-            # Angle 1: i-j-k 
-            n_ji = np.linalg.norm(vec_ji)
-            n_jk = r_jk # already calculated
-            
-            # Avoid division by zero if atoms overlap
-            if n_ji < 1e-8 or n_jk < 1e-8: continue
-            
-            cos_theta1 = np.dot(vec_ji, vec_jk) / (n_ji * n_jk)
-            
-            # Angle 2: j-k-l (Note: vec_kj is -vec_jk)
-            vec_kj = -vec_jk
-            n_kl = np.linalg.norm(vec_kl)
-            
-            if n_kl < 1e-8: continue
-            
-            cos_theta2 = np.dot(vec_kj, vec_kl) / (n_jk * n_kl)
+            n_ji, n_jk, n_kl = np.linalg.norm(vec_ji), np.linalg.norm(vec_jk), np.linalg.norm(vec_kl)
+            if min(n_ji, n_jk, n_kl) < 0.1: continue
 
-            # --- Damping Factor Calculation ---
-            # The Wilson B-matrix contains 1/sin(theta) terms which diverge at 180 deg.
-            # We scale the force constant by sin^2(theta) to cancel this divergence.
-            # sin^2(theta) = 1 - cos^2(theta)
+            # Cosine check for linearity: i-j-k and j-k-l
+            cos1 = np.dot(vec_ji, vec_jk) / (n_ji * n_jk)
+            cos2 = np.dot(-vec_jk, vec_kl) / (n_jk * n_kl)
             
-            sin2_theta1 = 1.0 - min(cos_theta1**2, 1.0)
-            sin2_theta2 = 1.0 - min(cos_theta2**2, 1.0)
+            # Use sin^2 to dampen force constant as it approaches linearity
+            sin2_1 = 1.0 - min(cos1**2, 1.0)
+            sin2_2 = 1.0 - min(cos2**2, 1.0)
             
-            # Hard cutoff: If geometry is extremely linear, skip to avoid NaN
-            if sin2_theta1 < 1e-4 or sin2_theta2 < 1e-4:
+            if sin2_1 < 1e-3 or sin2_2 < 1e-3:
                 continue
 
-            # Apply scaling factor
-            # This ensures the force constant goes to 0 as the angle becomes linear
-            scaling_factor = sin2_theta1 * sin2_theta2
-            force_const *= scaling_factor
-            
-            # --------------------------------------------------------
-
-            t_xyz = np.array([coord[i], coord[j], coord[k], coord[l]])
+            # Damping factor
+            scaling = sin2_1 * sin2_2
             
-            try:
-                tau, b_vec = torsion2(t_xyz)
-            except (ValueError, ArithmeticError):
-                # Skip if numerical errors occur in torsion calculation
-                continue
+            bond_sum = neighbor_counts[j] + neighbor_counts[k] - 2
+            r_cov_jk = covalent_radii_lib(element_list[j]) + covalent_radii_lib(element_list[k])
             
-            # Optimized: Use NumPy slicing and outer product
-            atoms = [i, j, k, l]
-            
-            for m_idx, m_atom in enumerate(atoms):
-                for n_idx, n_atom in enumerate(atoms):
-                    start_m, end_m = 3 * m_atom, 3 * m_atom + 3
-                    start_n, end_n = 3 * n_atom, 3 * n_atom + 3
-                    
-                    H_mn_block = force_const * np.outer(b_vec[m_idx], b_vec[n_idx])
-                    self.cart_hess[start_m:end_m, start_n:end_n] += H_mn_block
+            fc = self.calc_dihedral_force_const(n_jk, r_cov_jk, bond_sum)
+            fc *= scaling
 
-    # --- Optimized: Block assignment using slicing (and fixed logic) ---
-    def d3_dispersion_hessian(self, coord, element_list, bond_mat):
-        """Calculate Hessian correction based on D3 dispersion forces (Optimized/Corrected)"""
-        n_atoms = len(coord)
-        
-        # Calculate D3 dispersion correction for all atom pairs (i > j)
-        for i in range(n_atoms):
-            for j in range(i):
-                # Skip bonded atom pairs
-                if bond_mat[i, j]:
-                    continue
-                    
-                r_vec = coord[i] - coord[j]
-                r_ij = np.linalg.norm(r_vec)
+            try:
+                t_xyz = np.array([coord[i], coord[j], coord[k], coord[l]])
+                _, b_vec = torsion2(t_xyz)
                 
-                if r_ij < 0.1:
+                if not np.all(np.isfinite(b_vec)):
                     continue
-                
-                # Calculate D3 Hessian contribution (3x3 block)
-                hess_block = self.d3_hessian_contribution(r_vec, r_ij, element_list[i], element_list[j])
-                
-                # Use slicing for efficient block assignment
-                # H_ii += H_block, H_jj += H_block, H_ij -= H_block, H_ji -= H_block
-                start_i, end_i = 3 * i, 3 * i + 3
-                start_j, end_j = 3 * j, 3 * j + 3
-                
-                self.cart_hess[start_i:end_i, start_i:end_i] += hess_block
-                self.cart_hess[start_j:end_j, start_j:end_j] += hess_block
-                self.cart_hess[start_i:end_i, start_j:end_j] -= hess_block
-                self.cart_hess[start_j:end_j, start_i:end_i] -= hess_block
-    
-    # --- Optimized: Main function flow ---
+
+                atoms = [i, j, k, l]
+                for m_idx, m_atom in enumerate(atoms):
+                    for n_idx, n_atom in enumerate(atoms):
+                        block = fc * np.outer(b_vec[m_idx], b_vec[n_idx])
+                        self._add_block(m_atom, n_atom, block)
+            except Exception:
+                continue
+
     def main(self, coord, element_list, cart_gradient):
-        """
-        Calculate Hessian combining Fischer model and D3 dispersion correction
-        """
-        print("Generating Hessian using Fischer model with D3 dispersion correction...")
+        print("Generating Hessian using Fischer model with Dynamic D3 correction (Robust)...")
         
         n_atoms = len(coord)
         self.cart_hess = np.zeros((n_atoms*3, n_atoms*3), dtype="float64")
         
-        # Calculate bond connectivity matrix ONCE (Optimized internally)
-        bond_mat, dist_mat, pair_cov_radii_mat = self.get_bond_connectivity(coord, element_list)
+        # 1. Topology
+        BC = BondConnectivity()
+        bond_mat = BC.bond_connect_matrix(element_list, coord)
+        bond_indices = BC.bond_connect_table(bond_mat)
+        angle_indices = BC.angle_connect_table(bond_mat)
+        dihedral_indices = BC.dihedral_angle_connect_table(bond_mat)
         
-        # Calculate Hessian components from Fischer model (Optimized internally with slicing)
-        self.fischer_bond(coord, element_list)
-        self.fischer_angle(coord, element_list)
-        self.fischer_dihedral(coord, element_list, bond_mat)
+        # 2. Dynamic D3 Parameters (Coordination Numbers)
+        cn_list = self.calc_coordination_numbers(coord, element_list)
         
-        # Calculate Hessian components from D3 dispersion correction (Optimized internally with slicing)
-        self.d3_dispersion_hessian(coord, element_list, bond_mat)
+        # 3. Fischer Contributions (with strict linearity checks)
+        self.fischer_bond(coord, element_list, bond_indices)
+        self.fischer_angle(coord, element_list, angle_indices)
+        self.fischer_dihedral(coord, element_list, dihedral_indices, bond_mat)
         
-        # Optimized: Symmetrize the Hessian matrix
-        self.cart_hess = (self.cart_hess + self.cart_hess.T) / 2.0
+        # 4. Dynamic D3 Dispersion (Vectorized)
+        mask = np.tril(np.ones((n_atoms, n_atoms), dtype=bool), k=-1) & ~bond_mat
+        
+        diff_tensor = coord[:, None, :] - coord[None, :, :]  # (N, N, 3)
+        dist_matrix = np.linalg.norm(diff_tensor, axis=-1)
+        
+        mask &= (dist_matrix > 0.1)
+        i_idx, j_idx = np.where(mask)
+        
+        if len(i_idx) > 0:
+            # --- Pre-compute atomic parameters for all atoms (O(N)) ---
+            c6_atoms = np.array([D2_C6_coeff_lib(e) for e in element_list])
+            r4r2_atoms = np.array([self.d3_params.get_r4r2(e) for e in element_list])
+            ref_cn_atoms = np.array([self.ref_cn_map.get(e, 4) for e in element_list])
+            
+            # Safe VDW radii retrieval
+            vdw_atoms = np.zeros(n_atoms)
+            for k, e in enumerate(element_list):
+                try: vdw_atoms[k] = D2_VDW_radii_lib(e)
+                except: vdw_atoms[k] = covalent_radii_lib(e) * 1.5
+
+            # --- Gather Pair Data (O(M)) ---
+            r_vecs = diff_tensor[i_idx, j_idx]  # Vector r_ij (M, 3)
+            r_ijs = dist_matrix[i_idx, j_idx]   # Distance scalar (M,)
+            
+            # Dynamic C6 Scaling
+            cn_i = cn_list[i_idx]
+            cn_j = cn_list[j_idx]
+            scale_i = np.clip(1.0 - 0.05 * (cn_i - ref_cn_atoms[i_idx]), 0.75, 1.25)
+            scale_j = np.clip(1.0 - 0.05 * (cn_j - ref_cn_atoms[j_idx]), 0.75, 1.25)
+            
+            c6_ijs = np.sqrt((c6_atoms[i_idx] * scale_i) * (c6_atoms[j_idx] * scale_j))
+            
+            # C8 and R0
+            c8_ijs = 3.0 * c6_ijs * np.sqrt(r4r2_atoms[i_idx] * r4r2_atoms[j_idx])
+            r0s = vdw_atoms[i_idx] + vdw_atoms[j_idx]
+            
+            # --- Vectorized Gradient & Hessian Calculation ---
+            a1 = self.d3_params.a1
+            a2_6 = self.d3_params.a2
+            a2_8 = self.d3_params.a2 + 2.0
+            
+            # Damping terms
+            denom6 = r_ijs**6 + (a1 * r0s + a2_6)**6
+            denom8 = r_ijs**8 + (a1 * r0s + a2_8)**8
+            
+            f_damp6 = r_ijs**6 / denom6
+            f_damp8 = r_ijs**8 / denom8
+            
+            df_damp6 = 6 * r_ijs**5 / denom6 - 6 * r_ijs**12 / denom6**2
+            df_damp8 = 8 * r_ijs**7 / denom8 - 8 * r_ijs**16 / denom8**2
+            
+            # Gradients (Forces)
+            g6 = -self.d3_params.s6 * c6_ijs * ((-6.0/r_ijs**7)*f_damp6 + (1.0/r_ijs**6)*df_damp6)
+            g8 = -self.d3_params.s8 * c8_ijs * ((-8.0/r_ijs**9)*f_damp8 + (1.0/r_ijs**8)*df_damp8)
+            
+            # Second Derivatives (Projection coefficients)
+            h6_proj = self.d3_params.s6 * c6_ijs / r_ijs**8 * (42.0*f_damp6 - r_ijs*df_damp6)
+            h8_proj = self.d3_params.s8 * c8_ijs / r_ijs**10 * (72.0*f_damp8 - r_ijs*df_damp8)
+            
+            h_proj_vals = h6_proj + h8_proj
+            h_perp_vals = (g6 + g8) / r_ijs
+            
+            # Construct Hessian Blocks (M, 3, 3)
+            # P = u * u.T
+            unit_vecs = r_vecs / r_ijs[:, None]
+            proj_ops = np.einsum('bi,bj->bij', unit_vecs, unit_vecs) # (M, 3, 3)
+            identity = np.eye(3)[None, :, :]
+            
+            hess_blocks = h_proj_vals[:, None, None] * proj_ops + h_perp_vals[:, None, None] * (identity - proj_ops)
+            
+            # --- Accumulate into Cartesian Hessian ---
+            for k, (idx_i, idx_j) in enumerate(zip(i_idx, j_idx)):
+                block = hess_blocks[k]
+                self._add_block(idx_i, idx_i, block)
+                self._add_block(idx_j, idx_j, block)
+                self._add_block(idx_i, idx_j, -block)
+                self._add_block(idx_j, idx_i, -block)
         
-        # Project out rotational and translational modes
-        hess_proj = Calculationtools().project_out_hess_tr_and_rot_for_coord(self.cart_hess, element_list, coord)
+        # 5. Symmetrize & Clean
+        self.cart_hess = (self.cart_hess + self.cart_hess.T) / 2.0
         
+        # Project out TR/ROT modes
+        try:
+             hess_proj = Calculationtools().project_out_hess_tr_and_rot_for_coord(
+                 self.cart_hess, element_list, coord
+             )
+             if not np.all(np.isfinite(hess_proj)):
+                 print("Warning: Projection produced NaNs. Using unprojected Hessian.")
+                 hess_proj = self.cart_hess
+        except Exception as e:
+             print(f"Warning: Projection failed ({e}). Using unprojected Hessian.")
+             hess_proj = self.cart_hess
+             
+        if not np.all(np.isfinite(hess_proj)):
+             print("CRITICAL: Hessian contains NaNs after generation. Resetting to Identity.")
+             hess_proj = np.eye(n_atoms*3)
+
         return hess_proj