MultiOptPy 1.20.2__py3-none-any.whl

multioptpy/Optimizer/ric_rfo.py

@@ -0,0 +1,842 @@
+import numpy as np
+from scipy import linalg
+from multioptpy.Parameters.parameter import UnitValueLib, covalent_radii_lib
+from .hessian_update import ModelHessianUpdate
+
+"""
+Redundant Internal Coordinate RFO implementation
+Implementation without dihedral angles in primitive coordinates
+"""
+
+class RedundantInternalRFO:
+    def __init__(self, **config):
+        self.config = config
+        self.hess_update = ModelHessianUpdate()
+        
+        # Initialize RIC specific parameters
+        self.Initialization = True
+        self.saddle_order = self.config.get("saddle_order", 0)
+        self.trust_radius = float(self.config.get("trust_radius", 0.1))
+        self.trust_radius /= UnitValueLib().bohr2angstroms
+        self.DELTA = 0.1  # Step scale factor
+        
+        # For internal coordinate handling
+        self.B_matrix = None      # Wilson B matrix (transformation matrix)
+        self.G_matrix = None      # G matrix (metric matrix)
+        self.primitive_coords = None
+        
+        # RIC specific parameters
+        self.redundant_thresh = 1e-5   # Threshold for numerical stability
+        self.coord_type = self.config.get("coord_type", "redundant")
+        self.iter = 0
+        self.max_backsteps = 200
+        self.max_micro_cycles = 1000
+        self.FC_COUNT = self.config.get("FC_COUNT", -1)
+        self.backconv_method = self.config.get("backconv_method", "scf").lower()
+        
+        # Tracking variables
+        self.prev_cartesian = None
+        self.prev_gradient = None
+        self.internal_hessian = None
+        self.hessian = None
+        self.bias_hessian = None
+        self.prev_connectivity = None
+
+        self.element_list = self.config.get("element_list", None)
+    
+    def define_internal_coordinates(self, geometry):
+        """
+        Define primitive internal coordinates based on molecular connectivity
+        Returns the connectivity table and primitive internal coordinates
+        Using only bonds and angles (no dihedrals as requested)
+        """
+        atomic_numbers = self.element_list
+        # Convert geometry from (3N, 1) to (N, 3) format
+        natoms = len(atomic_numbers)
+        geom_reshaped = geometry.reshape(natoms, 3)
+        
+        primitive_coords = []
+        connectivity = np.zeros((natoms, natoms), dtype=int)
+        
+        # Build connectivity based on covalent radii
+        for i in range(natoms):
+            for j in range(i+1, natoms):
+                # Calculate distance between atoms
+                dist = np.linalg.norm(geom_reshaped[i] - geom_reshaped[j])
+                
+                # Get covalent radii based on atomic numbers
+                r_i = covalent_radii_lib(atomic_numbers[i])
+                r_j = covalent_radii_lib(atomic_numbers[j])
+                
+                # Check if atoms are bonded (using a bond tolerance factor of 1.2)
+                if dist < 1.2 * (r_i + r_j):
+                    connectivity[i, j] = 1
+                    connectivity[j, i] = 1
+                    
+                    # Add bond as primitive coordinate
+                    primitive_coords.append({
+                        'type': 'bond',
+                        'atoms': [i, j]
+                    })
+        
+        # Add angle coordinates
+        for j in range(natoms):
+            bonded_to_j = np.where(connectivity[j] > 0)[0]
+            for i in bonded_to_j:
+                for k in bonded_to_j:
+                    if i < k:  # Avoid duplicates
+                        primitive_coords.append({
+                            'type': 'angle',
+                            'atoms': [i, j, k]
+                        })
+        
+        # Note: As requested, no dihedral angles are added
+        
+        self.primitive_coords = primitive_coords
+        return connectivity, primitive_coords
+
+
+
+    def calc_center(self, geometry):
+        """Calculate center of mass of the geometry"""
+        n_atoms = len(geometry) // 3
+        return np.mean(geometry.reshape(n_atoms, 3), axis=0)
+    
+    def build_B_matrix(self, geometry, primitive_coords=None):
+        """
+        Build Wilson B matrix (∂q/∂x) for coordinate transformation
+        q: internal coordinates
+        x: Cartesian coordinates
+        
+        The geometry is expected in (3N, 1) format
+        """
+        if primitive_coords is None:
+            primitive_coords = self.primitive_coords
+            
+        natoms = len(geometry) // 3
+        geom_reshaped = geometry.reshape(natoms, 3)
+        ncoords = len(primitive_coords)
+        
+        B = np.zeros((ncoords, 3*natoms))
+        
+        for i, coord in enumerate(primitive_coords):
+            if coord['type'] == 'bond':
+                a1, a2 = coord['atoms']
+                B[i] = self._bond_B_elements(geom_reshaped, a1, a2)
+            elif coord['type'] == 'angle':
+                a1, a2, a3 = coord['atoms']
+                B[i] = self._angle_B_elements(geom_reshaped, a1, a2, a3)
+      
+        return B
+    
+    def _bond_B_elements(self, geometry, a1, a2):
+        """Calculate B matrix elements for bond stretching"""
+        r1 = geometry[a1]
+        r2 = geometry[a2]
+        
+        # Vector pointing from atom a1 to atom a2
+        vec = r2 - r1
+        
+        # Distance between the atoms
+        distance = np.linalg.norm(vec)
+        
+        if distance < 1e-10:
+            unit_vec = np.zeros(3)
+        else:
+            unit_vec = vec / distance
+            
+        # B matrix elements (derivatives of the bond distance w.r.t. Cartesian coordinates)
+        B_elements = np.zeros(3 * len(geometry))
+        
+        # For atom a1
+        B_elements[3*a1:3*a1+3] = -unit_vec
+        
+        # For atom a2
+        B_elements[3*a2:3*a2+3] = unit_vec
+        
+        return B_elements
+    
+    def _angle_B_elements(self, geometry, a1, a2, a3):
+        """Calculate B matrix elements for angle bending"""
+        r1 = geometry[a1]
+        r2 = geometry[a2]
+        r3 = geometry[a3]
+        
+        # Vectors from central atom to the other two atoms
+        v1 = r1 - r2
+        v3 = r3 - r2
+        
+        # Normalize vectors
+        d1 = np.linalg.norm(v1)
+        d3 = np.linalg.norm(v3)
+        
+        if d1 < 1e-10 or d3 < 1e-10:
+            return np.zeros(3 * len(geometry))
+            
+        v1_normalized = v1 / d1
+        v3_normalized = v3 / d3
+        
+        # Cosine of the angle
+        cos_angle = np.dot(v1_normalized, v3_normalized)
+        
+        # Ensure numerical stability
+        if cos_angle > 1.0:
+            cos_angle = 1.0
+        elif cos_angle < -1.0:
+            cos_angle = -1.0
+            
+        sin_angle = np.sqrt(1.0 - cos_angle**2)
+        
+        if sin_angle < 1e-10:
+            return np.zeros(3 * len(geometry))
+            
+        # Calculate derivatives
+        term1 = 1.0 / (d1 * sin_angle)
+        term3 = 1.0 / (d3 * sin_angle)
+        
+        # Cross products
+        cp1 = np.cross(v1_normalized, v3_normalized)
+        cp3 = np.cross(v3_normalized, v1_normalized)
+        
+        # B matrix elements
+        B_elements = np.zeros(3 * len(geometry))
+        
+        # For atom a1
+        B_elements[3*a1:3*a1+3] = term1 * cp1
+        
+        # For atom a3
+        B_elements[3*a3:3*a3+3] = term3 * cp3
+        
+        # For central atom a2
+        B_elements[3*a2:3*a2+3] = -(B_elements[3*a1:3*a1+3] + B_elements[3*a3:3*a3+3])
+        
+        return B_elements
+    
+    def build_G_matrix(self, B_matrix):
+        """
+        Build G matrix (metric matrix) from Wilson B matrix
+        G = B·B^T
+        """
+        G = np.dot(B_matrix, B_matrix.T)
+        return G
+    
+    def check_connectivity_change(self, geometry):
+        """
+        Check if the molecular connectivity has changed significantly
+        """
+        if self.prev_connectivity is None:
+            # First call, just store the current connectivity
+            connectivity, _ = self.define_internal_coordinates(geometry)
+            self.prev_connectivity = connectivity
+            return False
+        
+        # Check current connectivity
+        current_connectivity, _ = self.define_internal_coordinates(geometry)
+        
+        # Compare with previous connectivity matrix
+        diff = np.sum(np.abs(current_connectivity - self.prev_connectivity))
+        
+        # If there are changes in connectivity, reset coordinate system
+        if diff > 0:
+            print(f"WARNING: Detected {diff} changes in molecular connectivity")
+            print("Resetting internal coordinates due to bond rearrangement")
+            self.prev_connectivity = current_connectivity
+            return True
+        
+        return False
+    
+    def update_coordinates(self, geometry):
+        """
+        Update the internal coordinates for the current geometry
+        """
+        # Build B matrix for current geometry
+        B = self.build_B_matrix(geometry)
+        self.B_matrix = B
+        
+        # Build G matrix
+        G = self.build_G_matrix(B)
+        self.G_matrix = G
+        
+        return B
+    
+    def transform_gradient(self, cart_gradient):
+        """
+        Transform Cartesian gradient to internal coordinate gradient
+        g_int = B·g_cart (direct transformation using Wilson B matrix)
+        """
+        B = self.B_matrix
+        
+        # Direct transformation using B matrix
+        int_gradient = np.dot(B, cart_gradient)
+        return int_gradient
+    
+    def transform_hessian(self, cart_hessian):
+        """
+        Transform Cartesian Hessian to internal coordinate Hessian
+        H_int = B·H_cart·B^T (direct transformation)
+        """
+        B = self.B_matrix
+        
+        # Direct transformation
+        int_hessian = np.dot(B, np.dot(cart_hessian, B.T))
+        return int_hessian
+    
+    def internal_to_cartesian_scf(self, step_int, geometry, 
+                                max_iterations=100,
+                                convergence_threshold=1e-8):
+        """
+        SCF-inspired algorithm for internal to Cartesian coordinate conversion.
+        Uses techniques from electronic structure theory: line search when far from
+        convergence and Newton-Raphson near convergence, with DIIS acceleration.
+        
+        Parameters:
+        -----------
+        step_int : ndarray
+            Target step in internal coordinates
+        geometry : ndarray
+            Starting geometry in Cartesian coordinates
+        max_iterations : int
+            Maximum number of iterations
+        convergence_threshold : float
+            Convergence criterion for RMS error
+            
+        Returns:
+        --------
+        ndarray
+            Step in Cartesian coordinates
+        """
+        # Initialize variables
+        reference_geom = geometry.copy()
+        current_geom = geometry.copy()
+        best_geom = current_geom.copy()
+        best_error = float('inf')
+        
+        # DIIS parameters
+        diis_start = 3
+        diis_max = 8
+        diis_errors = []
+        diis_geometries = []
+        
+        # Dynamic algorithm control
+        use_newton = False  # Start with line search, switch to Newton later
+        damping_factor = 0.7  # Initial damping
+        level_shift = 0.0  # Level shifting parameter
+        
+        # Last iteration data for backtracks
+        prev_error = float('inf')
+        prev_geom = None
+        
+        # Calculate initial values
+        B = self.build_B_matrix(current_geom)
+        current_q = np.dot(B, current_geom - reference_geom)
+        delta_q = step_int - current_q
+        error = np.linalg.norm(delta_q)
+        rms_error = error / np.sqrt(len(delta_q))
+        
+        print(f"Starting SCF-like optimization: initial RMS error = {rms_error:.3e}")
+        
+        # Main iteration loop
+        for iteration in range(max_iterations):
+            # Save best solution
+            if error < best_error:
+                best_error = error
+                best_geom = current_geom.copy()
+            
+            # Report progress
+            if iteration % 20 == 0 or iteration < 2:
+                print(f"Iteration {iteration}: RMS error = {rms_error:.3e}, "
+                    f"{'Newton' if use_newton else 'LineSearch'}, damping={damping_factor:.2f}")
+            
+            # Check convergence
+            if rms_error < convergence_threshold:
+                print(f"Conversion converged in {iteration+1} iterations")
+                break
+            
+            # Prepare for this iteration
+            B = self.build_B_matrix(current_geom)
+            
+            # Calculate step based on current method
+            if use_newton:
+                # Calculate B+ (pseudoinverse of B) using SVD with level shifting
+                try:
+                    U, s, Vh = np.linalg.svd(B, full_matrices=False)
+                    
+                    # Apply level shifting to singular values (similar to SCF level shifting)
+                    s_inv = np.where(s > 1e-7, 1.0 / (s + level_shift), 0.0)
+                    
+                    B_pinv = np.dot(Vh.T * s_inv, U.T)
+                    
+                    # Calculate Newton step
+                    step = np.dot(B_pinv, delta_q)
+                except np.linalg.LinAlgError:
+                    # Fall back to a more stable approach
+                    print("SVD failed, using pinv with increased regularization")
+                    B_pinv = np.linalg.pinv(B, rcond=1e-6)
+                    step = np.dot(B_pinv, delta_q)
+            else:
+                # Line search along steepest descent direction
+                gradient = np.dot(B.T, delta_q)
+                grad_norm = np.linalg.norm(gradient)
+                
+                if grad_norm < 1e-10:
+                    # Gradient too small, try Newton step
+                    use_newton = True
+                    B_pinv = np.linalg.pinv(B, rcond=1e-7)
+                    step = np.dot(B_pinv, delta_q)
+                else:
+                    # Normalize gradient and scale by dynamic step size
+                    step_dir = gradient / grad_norm
+                    
+                    # Determine step size (larger when further from convergence)
+                    # Similar to trust radius in SCF
+                    step_size = min(0.2, 0.1 * (1.0 + 10.0 * rms_error))
+                    
+                    step = step_size * step_dir
+            
+            # Apply DIIS acceleration if we have enough iterations
+            diis_step = None
+            if iteration >= diis_start:
+                # Store current error and geometry for DIIS
+                diis_errors.append(delta_q.flatten())
+                diis_geometries.append(current_geom.copy())
+                
+                # Limit DIIS vector storage
+                if len(diis_errors) > diis_max:
+                    diis_errors.pop(0)
+                    diis_geometries.pop(0)
+                
+                # Apply DIIS if we have at least 2 vectors
+                if len(diis_errors) >= 2:
+                    try:
+                        diis_step = self._compute_diis_solution(diis_errors, diis_geometries)
+                    except Exception as e:
+                        print(f"DIIS failed: {e}")
+                        diis_step = None
+            
+            # Try step with current damping
+            damped_step = step * damping_factor
+            trial_geom = current_geom + damped_step
+            
+            # Evaluate trial geometry
+            trial_B = self.build_B_matrix(trial_geom)
+            trial_q = np.dot(trial_B, trial_geom - reference_geom)
+            trial_delta_q = step_int - trial_q
+            trial_error = np.linalg.norm(trial_delta_q)
+            trial_rms = trial_error / np.sqrt(len(trial_delta_q))
+            
+            # If we have a DIIS solution, evaluate it too
+            if diis_step is not None:
+                diis_B = self.build_B_matrix(diis_step)
+                diis_q = np.dot(diis_B, diis_step - reference_geom)
+                diis_delta_q = step_int - diis_q
+                diis_error = np.linalg.norm(diis_delta_q)
+                diis_rms = diis_error / np.sqrt(len(diis_delta_q))
+                
+                # Use DIIS if it's better
+                if diis_error < trial_error and diis_error < error:
+                    #print(f"DIIS improvement: {trial_rms:.3e} -> {diis_rms:.3e}")
+                    current_geom = diis_step
+                    delta_q = diis_delta_q
+                    error = diis_error
+                    rms_error = diis_rms
+                    
+                    # DIIS was successful, try to reduce level shifting
+                    if level_shift > 0:
+                        level_shift = max(0, level_shift * 0.5)
+                    continue  # Skip to next iteration
+            
+            # Dynamically adjust the algorithm based on progress
+            if trial_error < error:
+                # Step is good, accept it
+                current_geom = trial_geom
+                delta_q = trial_delta_q
+                prev_error = error
+                error = trial_error
+                rms_error = trial_rms
+                
+                # Increase damping for more aggressive steps
+                damping_factor = min(1.0, damping_factor * 1.2)
+                
+                # Switch to Newton method when close enough to solution
+                if not use_newton and rms_error < 0.1:
+                    #print(f"Switching to Newton-Raphson at iteration {iteration+1}")
+                    use_newton = True
+                    
+                # Reduce level shifting since things are going well
+                if level_shift > 0:
+                    level_shift = max(0, level_shift * 0.5)
+                    
+            else:
+                # Step is bad, adjust strategy
+                if use_newton:
+                    # Newton step made things worse
+                    if level_shift == 0:
+                        # Start with modest level shifting
+                        level_shift = 0.1
+                    else:
+                        # Increase level shifting (similar to SCF when oscillating)
+                        level_shift = min(1.0, level_shift * 2.0)
+                        
+                    #print(f"Increasing level shift to {level_shift:.3e}")
+                    
+                    # If level shift is getting too high, try line search
+                    if level_shift > 0.5:
+                        #print("Switching to line search due to unstable Newton steps")
+                        use_newton = False
+                
+                # Reduce damping for more conservative steps
+                damping_factor = max(0.2, damping_factor * 0.5)
+                
+                # If we have previous good geometry, backtrack halfway
+                if prev_geom is not None:
+                    #print(f"Backtracking: {error:.3e} -> {prev_error:.3e}")
+                    current_geom = 0.5 * (current_geom + prev_geom)
+                    
+                    # Recalculate at backtracked position
+                    B = self.build_B_matrix(current_geom)
+                    current_q = np.dot(B, current_geom - reference_geom)
+                    delta_q = step_int - current_q
+                    error = np.linalg.norm(delta_q)
+                    rms_error = error / np.sqrt(len(delta_q))
+                
+            # Save current position for potential backtracking
+            prev_geom = current_geom.copy()
+        
+        # Handle non-convergence
+        if iteration == max_iterations - 1 and rms_error > convergence_threshold:
+            print(f"Warning: Conversion did not converge. Best RMS error = {best_error/np.sqrt(len(step_int)):.3e}")
+            current_geom = best_geom
+        
+        # Return the Cartesian step
+        return current_geom - reference_geom
+
+    def _compute_diis_solution(self, error_vectors, geometries):
+        """
+        Compute DIIS extrapolated solution using Pulay's method
+        
+        Parameters:
+        -----------
+        error_vectors : list
+            List of error vectors (flattened)
+        geometries : list
+            List of corresponding geometries
+            
+        Returns:
+        --------
+        ndarray
+            DIIS extrapolated geometry
+        """
+        n_vecs = len(error_vectors)
+        
+        # Build DIIS B matrix for Pulay method
+        B_diis = np.zeros((n_vecs + 1, n_vecs + 1))
+        
+        # Fill error vector dot products
+        for i in range(n_vecs):
+            for j in range(n_vecs):
+                B_diis[i, j] = np.dot(error_vectors[i], error_vectors[j])
+        
+        # Add constraint rows/columns
+        B_diis[n_vecs, :n_vecs] = 1.0
+        B_diis[:n_vecs, n_vecs] = 1.0
+        B_diis[n_vecs, n_vecs] = 0.0
+        
+        # RHS vector [0,0,...,0,1]
+        rhs = np.zeros(n_vecs + 1)
+        rhs[n_vecs] = 1.0
+        
+        # Add small regularization to diagonal for numerical stability
+        for i in range(n_vecs):
+            B_diis[i, i] += 1e-8 * (1.0 + abs(B_diis[i, i]))
+        
+        # Solve DIIS equations
+        try:
+            c = np.linalg.solve(B_diis, rhs)
+        except np.linalg.LinAlgError:
+            # Use SVD-based solution if direct solve fails
+            c = np.linalg.lstsq(B_diis, rhs, rcond=1e-10)[0]
+        
+        # Construct DIIS solution
+        diis_geom = np.zeros_like(geometries[0])
+        for i in range(n_vecs):
+            diis_geom += c[i] * geometries[i]
+            
+        return diis_geom
+        
+    
+    def _evaluate_error(self, geom, reference_geom, target_step):
+        """
+        Helper function to evaluate the error for a given geometry
+        """
+        B = self.build_B_matrix(geom)
+        current_q = np.dot(B, geom - reference_geom)
+        delta_q = target_step - current_q
+        return np.linalg.norm(delta_q)
+
+
+    def internal_to_cartesian(self, step_int, geometry):
+        """
+        Transform step in internal coordinates to Cartesian coordinates
+        using enhanced iterative methods
+        """
+        # Choose the algorithm based on configuration or problem characteristics
+        
+        if self.backconv_method == "scf":
+            return self.internal_to_cartesian_scf(step_int, geometry)
+        else:  
+            return self.internal_to_cartesian_scf(step_int, geometry)
+    
+    def get_cleaned_hessian(self, hessian):
+        """Ensure the Hessian is clean and well-conditioned"""
+        # Ensure symmetry
+        hessian = 0.5 * (hessian + hessian.T)
+        
+        try:
+            # Use more stable eigenvalue decomposition
+            eigval, eigvec = linalg.eigh(hessian)
+        except np.linalg.LinAlgError:
+            # Fallback to more robust algorithm if standard fails
+            print("Warning: Using more robust eigenvalue decomposition")
+            eigval, eigvec = linalg.eigh(hessian, driver='evr')
+        
+        # Find valid eigenvalues (|λ| > 1e-7)
+        valid_mask = np.abs(eigval) > 1e-7
+        n_removed = np.sum(~valid_mask)
+        
+        # Create diagonal matrix with only valid eigenvalues
+        # Replace small eigenvalues with small positive values
+        cleaned_eigval = np.where(valid_mask, eigval, 1e-7)
+        
+        # Reconstruct Hessian using only valid components
+        # H = U Λ U^T where Λ contains only valid eigenvalues
+        cleaned_hessian = np.dot(np.dot(eigvec, np.diag(cleaned_eigval)), eigvec.T)
+        
+        # Ensure symmetry of final result
+        cleaned_hessian = 0.5 * (cleaned_hessian + cleaned_hessian.T)
+        
+        return cleaned_hessian, n_removed
+    
+    def run_rfo_step(self, int_gradient, int_hessian):
+        """
+        Calculate the RFO step in internal coordinates with improved stability
+        """
+        n_coords = len(int_gradient)
+        
+        # Ensure symmetry and clean the Hessian
+        new_hess = 0.5 * (int_hessian + int_hessian.T)
+        new_hess, _ = self.get_cleaned_hessian(new_hess)
+        
+        # Construct RFO matrix
+        matrix_for_RFO = np.block([
+            [new_hess, int_gradient.reshape(n_coords, 1)],
+            [int_gradient.reshape(1, n_coords), np.zeros((1, 1))]
+        ])
+        
+        # Get eigenvalues of the RFO matrix
+        try:
+            RFO_eigenvalues, RFO_eigenvectors = linalg.eigh(matrix_for_RFO)
+        except np.linalg.LinAlgError:
+            print("Warning: Using more robust eigenvalue algorithm")
+            RFO_eigenvalues, RFO_eigenvectors = linalg.eigh(matrix_for_RFO, driver='evr')
+        
+        # Sort eigenvalues
+        idx = np.argsort(RFO_eigenvalues)
+        RFO_eigenvalues = RFO_eigenvalues[idx]
+        RFO_eigenvectors = RFO_eigenvectors[:, idx]
+        
+        # Select appropriate eigenvalue based on saddle order
+        lambda_for_calc = float(RFO_eigenvalues[self.saddle_order])
+        
+        # Calculate step using direct RFO approach
+        shifted_hessian = new_hess - lambda_for_calc * np.eye(n_coords)
+        
+        # Solve the RFO equations
+        try:
+            # LU decomposition for stable solving
+            move_vector = -np.linalg.solve(shifted_hessian, int_gradient)
+        except np.linalg.LinAlgError:
+            print("Warning: Linear solve failed, using pseudoinverse")
+            # Use pseudoinverse as fallback
+            shifted_hessian_inv = np.linalg.pinv(shifted_hessian, rcond=1e-10)
+            move_vector = -np.dot(shifted_hessian_inv, int_gradient)
+        
+        print(f"Lambda for RFO step: {lambda_for_calc}")
+        print(f"Gradient RMS: {np.sqrt(np.mean(int_gradient**2))}")
+        print(f"Step RMS: {np.sqrt(np.mean(move_vector**2))}")
+        
+        # Limit step size if it exceeds trust radius
+        step_norm = np.linalg.norm(move_vector)
+        if step_norm > self.trust_radius:
+            scale_factor = self.trust_radius / step_norm
+            move_vector *= scale_factor
+            print(f"Step scaled by {scale_factor} to meet trust radius")
+        
+        return move_vector.reshape(-1, 1)
+    
+    def reset_system(self, geometry):
+        """
+        Reset internal coordinates when molecular structure changes significantly
+        """
+        print("Resetting redundant internal coordinate system")
+        
+        # Clear previous coordinates
+        self.primitive_coords = None
+        
+        # Define new internal coordinates
+        _, self.primitive_coords = self.define_internal_coordinates(geometry)
+        print(f"Defined {len(self.primitive_coords)} new primitive coordinates")
+        
+        # Update B matrix
+        B = self.update_coordinates(geometry)
+        
+        # Reset Hessian to identity
+        self.internal_hessian = np.eye(len(self.primitive_coords))
+        self.Initialization = False
+        
+        return B
+    
+    def run(self, geom_num_list, B_g, pre_B_g, pre_geom, B_e, pre_B_e, pre_move_vector, initial_geom_num_list, g, pre_g):
+        """
+        Main optimization step function using Redundant Internal Coordinates
+        """
+        print(f"======= RIC-RFO Iteration {self.iter} =======")
+        
+        # Define internal coordinates if not already defined
+        if self.primitive_coords is None:
+            _, self.primitive_coords = self.define_internal_coordinates(geom_num_list)
+            print(f"Defined {len(self.primitive_coords)} primitive internal coordinates")
+        
+        # Check if molecular connectivity has changed
+        coords_reset = False
+        if pre_geom is not None:
+            coords_reset = self.check_connectivity_change(geom_num_list)
+        
+        if coords_reset:
+            # Reset coordinate system if connectivity changed
+            B = self.reset_system(geom_num_list)
+        else:
+            # Update coordinate system for current geometry
+            B = self.update_coordinates(geom_num_list)
+        
+        # Transform gradient to internal coordinates
+        int_gradient = self.transform_gradient(B_g)
+        
+        # Initialize or update the Hessian
+        if self.Initialization or self.internal_hessian is None:
+            # Start with identity Hessian in internal coordinates
+            self.internal_hessian = np.eye(len(self.primitive_coords))
+            self.Initialization = False
+        else:
+            # Update the internal coordinate Hessian if we have previous geometry and gradient
+            if pre_geom is not None and pre_B_g is not None and not coords_reset:
+                # Calculate previous internal gradient
+                prev_B = self.build_B_matrix(pre_geom)
+                prev_G = self.build_G_matrix(prev_B)
+                
+                try:
+                    U, s, Vh = np.linalg.svd(prev_G, full_matrices=False)
+                    s_inv = np.array([1.0/x if x > self.redundant_thresh else 0.0 for x in s])
+                    G_inv = np.dot(U * s_inv[:, np.newaxis], U.T)
+                    
+                    prev_B_pinv = np.dot(G_inv, prev_B)
+                except np.linalg.LinAlgError:
+                    prev_B_pinv = np.linalg.pinv(prev_B, rcond=1e-8)
+                
+                prev_int_gradient = np.dot(prev_B_pinv, pre_B_g)
+                
+                # Calculate displacement in internal coordinates
+                cart_displacement = (geom_num_list - pre_geom).reshape(-1, 1)
+                int_displacement = np.dot(B, cart_displacement)
+                
+                # Delta gradient in internal coordinates
+                delta_grad = (int_gradient - prev_int_gradient).reshape(-1, 1)
+                
+                # Update Hessian using the hess_update methods
+                if "msp" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using MSP Hessian update")
+                    delta_hess = self.hess_update.MSP_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                elif "bfgs" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using BFGS Hessian update")
+                    delta_hess = self.hess_update.BFGS_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                elif "fsb" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using FSB Hessian update")
+                    delta_hess = self.hess_update.FSB_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                elif "bofill" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using Bofill Hessian update")
+                    delta_hess = self.hess_update.Bofill_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                elif "sr1" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using SR1 Hessian update")
+                    delta_hess = self.hess_update.SR1_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                elif "psb" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using PSB Hessian update")
+                    delta_hess = self.hess_update.PSB_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                elif "flowchart" in self.config.get("method", "").lower():
+                    print("RIC-RFO: Using flowchart Hessian update")
+                    delta_hess = self.hess_update.flowchart_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad, self.config["method"]
+                    )
+                else:
+                    # Default to BFGS if no method is specified
+                    print("RIC-RFO: Using BFGS Hessian update (default)")
+                    delta_hess = self.hess_update.BFGS_hessian_update(
+                        self.internal_hessian, int_displacement, delta_grad
+                    )
+                
+                # Apply the Hessian update
+                self.internal_hessian += delta_hess
+        
+        # Ensure the Hessian is symmetric
+        self.internal_hessian = 0.5 * (self.internal_hessian + self.internal_hessian.T)
+        
+        # Apply bias Hessian if provided
+        working_hessian = self.internal_hessian.copy()
+        if self.bias_hessian is not None:
+            int_bias_hessian = self.transform_hessian(self.bias_hessian)
+            working_hessian += int_bias_hessian
+        
+        # Calculate RFO step in internal coordinates
+        int_step = self.run_rfo_step(int_gradient, working_hessian)
+        
+        # Transform step back to Cartesian coordinates
+        cart_step = self.internal_to_cartesian(int_step, geom_num_list)
+        
+        # Store current state for next iteration
+        self.prev_cartesian = geom_num_list.copy()
+        self.prev_gradient = B_g.copy()
+        
+        # Increment iteration counter
+        self.iter += 1
+        
+        # Apply DELTA scaling and reshape
+        return -1 * self.DELTA * cart_step.reshape(-1, 1)
+    
+    def set_hessian(self, hessian):
+        """Set Cartesian Hessian"""
+        self.hessian = hessian.copy()
+        if self.B_matrix is not None:
+            # Transform to internal coordinates
+            self.internal_hessian = self.transform_hessian(hessian)
+        
+    def set_bias_hessian(self, bias_hessian):
+        """Set bias Hessian (in Cartesian coordinates)"""
+        self.bias_hessian = bias_hessian.copy()
+    
+    def get_hessian(self):
+        """Return current Hessian (in Cartesian coordinates)"""
+        return self.hessian if self.hessian is not None else None
+    
+    
+    def get_bias_hessian(self):
+        return self.bias_hessian