kmclab 0.1.0__py3-none-any.whl

kmclab/hex.py

@@ -0,0 +1,1072 @@
+import numpy as np
+from matplotlib.animation import FuncAnimation, PillowWriter
+import matplotlib.cm as cm
+from numpy.polynomial.polynomial import Polynomial
+import matplotlib.pyplot as plt
+import matplotlib.patches as patches
+from scipy.stats import linregress
+from __future__ import annotations       
+
+
+class hex_kmc:
+    
+    def __init__(self, n_atoms, n_defects, n_adsorbates, lattice_size, n_steps, defect_type = 1, adsorbates_freq = -1,  seed=1):
+        
+        np.random.seed(seed)    
+        # what is you desired coverage= n_atom/lattice * lattice
+        self.n_atoms = n_atoms  # Number of atoms
+        self.n_defects = n_defects
+        self.n_adsorbates= n_adsorbates
+        self.lattice_size = lattice_size  # Lattice size
+        self.n_steps = n_steps # Number of steps
+        self.defect_type = defect_type
+        self.adsorbates_freq = adsorbates_freq
+  
+        T = 300  # Temperature in Kelvin
+        k_B = 8.617e-5  # Boltzmann constant in eV/K
+        k_0 = 1
+        h = 4.1357e-15  #Planck Constant (eV.s)
+        self.len_vertical = 0.38e-3 # in micrometer
+        self.len_horizontal = 0.51e-3 # in micrometer
+    
+
+        # DFT calculated vaues for diffusion on the stoichiometric surface in different directions (eV)
+        energy_barrier_north = 0.46
+        energy_barrier_south = 0.46
+        energy_barrier_northeast = 0.65
+        energy_barrier_northwest = 0.65
+        energy_barrier_southeast = 0.65
+        energy_barrier_southwest = 0.65
+
+
+        # DFT calculated vaues for diffusion out of trapping deffect in different directions (eV)
+        energy_barrier_trapping_defect_north = 1.2
+        energy_barrier_trapping_defect_south = 1.2
+        energy_barrier_trapping_defect_east = 1.1
+        energy_barrier_trapping_defect_west = 1.1       
+        energy_barrier_trapping_defect_northeast = 1.1
+        energy_barrier_trapping_defect_northwest = 1.1
+        energy_barrier_trapping_defect_southeast = 1.1
+        energy_barrier_trapping_defect_southwest = 1.1
+
+        
+        # DFT calculated vaues for diffusion over a blocking deffect in different directions (eV)
+        energy_barrier_blocking_defect_north = 1.2
+        energy_barrier_blocking_defect_south = 1.2    
+        energy_barrier_blocking_defect_northeast = 1.2
+        energy_barrier_blocking_defect_northwest = 1.2
+        energy_barrier_blocking_defect_southeast = 1.2
+        energy_barrier_blocking_defect_southwest = 1.2
+        # DFT calculated vaues for diffusion over an adsorbate in different directions (eV)
+        
+        energy_barrier_adsorbate_north = 0.72
+        energy_barrier_adsorbate_south = 0.72 
+        energy_barrier_adsorbate_northeast = 0.72        
+        energy_barrier_adsorbate_northwest = 0.72
+        energy_barrier_adsorbate_southeast = 0.72
+        energy_barrier_adsorbate_southwest = 0.72        
+        
+                      
+        # Calculate rate constants
+        rate_north = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_north / (k_B * T))
+        rate_south = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_south / (k_B * T))
+        rate_northeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_northeast / (k_B * T))
+        rate_northwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_northwest / (k_B * T))
+        rate_southeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_southeast / (k_B * T))
+        rate_southwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_southwest / (k_B * T))
+        
+        rate_trapping_defect_north = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_north / (k_B * T))
+        rate_trapping_defect_south = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_south / (k_B * T))
+        rate_trapping_defect_east = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_east / (k_B * T))
+        rate_trapping_defect_west = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_west / (k_B * T))
+        rate_trapping_defect_northeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_northeast / (k_B * T))
+        rate_trapping_defect_northwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_northwest / (k_B * T))
+        rate_trapping_defect_southeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_southeast / (k_B * T))
+        rate_trapping_defect_southwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_trapping_defect_southwest / (k_B * T))
+       
+   
+        rate_blocking_defect_north = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_blocking_defect_north / (k_B * T))
+        rate_blocking_defect_south = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_blocking_defect_south / (k_B * T))
+        rate_blocking_defect_northeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_blocking_defect_northeast / (k_B * T))
+        rate_blocking_defect_northwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_blocking_defect_northwest / (k_B * T))
+        rate_blocking_defect_southeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_blocking_defect_southeast / (k_B * T))
+        rate_blocking_defect_southwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_blocking_defect_southwest / (k_B * T))
+       
+        rate_adsorbate_north = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_adsorbate_north / (k_B * T))
+        rate_adsorbate_south = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_adsorbate_south / (k_B * T))         
+        rate_adsorbate_northeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_adsorbate_northeast / (k_B * T))
+        rate_adsorbate_northwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_adsorbate_northwest / (k_B * T))
+        rate_adsorbate_southeast = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_adsorbate_southeast / (k_B * T))
+        rate_adsorbate_southwest = k_0 * ((k_B * T)/h) * np.exp(-energy_barrier_adsorbate_southwest / (k_B * T))
+       
+  
+        self.moves = {
+            "north": (0, 1),
+            "south": (0, -1),
+            "northeast": (1, 0.5),
+            "southeast": (1, -0.5),
+            "northwest": (-1, 0.5),
+            "southwest": (-1, -0.5)
+        }
+
+        self.move_rates = {
+            "north": rate_north,
+            "south": rate_south,
+            "northeast": rate_northeast,
+            "southeast": rate_northwest,
+            "northwest": rate_southeast,
+            "southwest": rate_southwest
+        }
+  
+        self.move_rates_trapping_defects = {
+            "north": rate_trapping_defect_north,
+            "south": rate_trapping_defect_south,
+            "east": rate_trapping_defect_east,
+            "west": rate_trapping_defect_west,           
+            "northeast": rate_trapping_defect_northeast, 
+            "northwest": rate_trapping_defect_northwest, 
+            "southeast": rate_trapping_defect_southeast, 
+            "southwest": rate_trapping_defect_southwest
+        }        
+                   
+        self.move_rates_blocking_defects = {
+            "north": rate_blocking_defect_north,
+            "south": rate_blocking_defect_south,
+            "northeast": rate_blocking_defect_northeast, 
+            "northwest": rate_blocking_defect_northwest, 
+            "southeast": rate_blocking_defect_southeast, 
+            "southwest": rate_blocking_defect_southwest
+        }        
+        
+        self.move_rates_adsorbates = {
+            "north": rate_adsorbate_north,
+            "south": rate_adsorbate_south,
+            "northeast":  rate_adsorbate_northeast,
+            "southeast":  rate_adsorbate_northwest,
+            "northwest":  rate_adsorbate_southeast,
+            "southwest":  rate_adsorbate_southwest
+        }
+
+        
+        self.hex_lattice()
+        
+        self.generate_defects()
+
+        self.init_atoms()
+        
+        self.generate_adsorbates()
+        
+    def run(self):
+        
+        self.time = np.zeros(self.n_steps + 1)
+        self.msd = np.zeros(self.n_steps)
+        self.md = np.zeros(self.n_steps)
+        self.positions_over_time = []
+        self.positions_adsorbates_over_time = []
+
+        k_tot_rec = np.zeros(self.n_steps)
+
+        self.selected_moves_info = []
+        
+        move_counts = {move: 0 for move in self.moves}
+        defects_sites = {site for pair in self.defects_pairs for site in pair}  
+        
+        
+        if self.defect_type == 1:
+        
+            for step in range(self.n_steps):
+                            
+                if self.adsorbates_freq != -1:
+                    if step % int(self.adsorbates_freq) == 0:
+                        self.generate_adsorbates()
+                    
+                self.positions_over_time.append(self.positions_atoms.copy())  # Store positions at each step
+                self.positions_adsorbates_over_time.append(self.positions_adsorbates.copy())  # Store hy positions at each step
+                atom_occupied_sites = {tuple(pos) for pos in self.positions_atoms}  # Track occupied sites, position and occupoied sites are the same but different type
+                adsorbates_occupied_sites = {tuple(pos) for pos in self.positions_adsorbates}
+                
+                defects_occ_sites = []
+                for atom_idx, (x, y) in enumerate(self.positions_atoms):
+                    defect = False
+                    for pair in self.defects_pairs:
+                        if (x,y) in pair:
+                            defect = True
+                            break
+                    if defect:
+                       defects_occ_sites.append(pair[0])
+                       defects_occ_sites.append(pair[1])
+                       
+                defects_occupied_sites = {tuple(pos) for pos in defects_occ_sites}
+                
+                total_rate = 0
+                possible_moves = []
+    
+                for atom_idx, (x, y) in enumerate(self.positions_atoms):
+                        
+                    # is ov?
+                    defect = False
+                    for pair in self.defects_pairs:
+                        if (x,y) in pair:
+                            defect = True
+                            break
+                        
+                        
+                    if defect:
+                        
+                        pair = self.find_pair((x,y), self.defects_pairs)
+                        move_defects_predicted= self.move_defects(pair, self.lattice_size)
+                        
+                        for dir_idx, (direction, (new_x, new_y)) in enumerate(move_defects_predicted.items()):
+                            
+                            new_position = (new_x, new_y)
+                            
+                                
+                            if (new_x, new_y) not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites and (new_x, new_y) not in adsorbates_occupied_sites:
+                                   if direction == 'north':
+                                       dx = 0
+                                       dy = 1.5
+                                       total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]  
+                                       possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                   elif direction == 'south':
+                                       dx = 0
+                                       dy = - 1.5
+                                       total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]
+                                       possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx],(new_x, new_y), dx, dy))
+                                   elif direction == 'east':
+                                       dx = 1
+                                       dy = 0
+                                       total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]
+                                       possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                   elif direction == 'west':
+                                        dx = -1
+                                        dy = 0
+                                        total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]
+                                        possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                        
+                                   elif direction == 'northeast':
+                                        dx = 1
+                                        dy = 1
+                                        total_rate += list(self.move_rates_trapping_defects.values())[dir_idx] 
+                                        possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                          
+                                   elif direction == 'northwest':
+                                        dx = -1
+                                        dy = 1
+                                        total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]
+                                        possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                          
+                                   elif direction == 'southeast':
+                                        dx = 1
+                                        dy = -1
+                                        total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]
+                                        possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                          
+                                   elif direction == 'southwest':
+                                        dx = -1
+                                        dy = -1
+                                        total_rate += list(self.move_rates_trapping_defects.values())[dir_idx]
+                                        possible_moves.append((atom_idx, dir_idx, list(self.move_rates_trapping_defects.values())[dir_idx], (new_x, new_y), dx, dy))
+                                            
+                                                        
+    
+                     
+                    else:     
+                    
+                        for dir_idx, (dx, dy) in enumerate(list(self.moves.values())):
+                
+                            new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                            new_position = (new_x, new_y)
+                              
+                            if new_position in adsorbates_occupied_sites:
+                                
+                                dx = 2 * dx
+                                dy = 2 * dy
+                                new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                                new_position = (new_x, new_y)
+                                if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites and (new_x, new_y) not in adsorbates_occupied_sites:
+                                    total_rate += list(self.move_rates_adsorbates.values())[dir_idx]
+                                    possible_moves.append((atom_idx, dir_idx, list(self.move_rates_adsorbates.values())[dir_idx], (new_x, new_y), dx, dy))    
+                                
+                            else:
+                                
+                                if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites:
+                                    total_rate += list(self.move_rates.values())[dir_idx]
+                                    possible_moves.append((atom_idx, dir_idx, list(self.move_rates.values())[dir_idx], (new_x, new_y), dx, dy))    
+                    
+                rho1, rho2 = np.random.random(), np.random.random()
+    
+                k_tot = total_rate
+                
+                cumulative_rate = 0
+                for move_idx, (atom_idx, dir_idx, rate, new_pos, _, _) in enumerate(possible_moves):
+                    cumulative_rate += rate
+                    if rho1 * k_tot < cumulative_rate:
+                        selected_move = move_idx
+                        break
+                
+                # Execute the selected process
+                 
+                atom_idx, dir_idx, rate, (new_x, new_y), dx, dy = possible_moves[selected_move]
+                
+                if step % int(self.n_steps/10) == 0:
+                    print(f'step = {step}')
+                    
+                # print(f'atom_{atom_idx} moves: dx = {dx}, dy = {dy}')
+                self.cumulative_vectors[atom_idx, 0] += dx
+                self.cumulative_vectors[atom_idx, 1] += dy
+                atom_occupied_sites.remove(self.positions_atoms[atom_idx])
+                self.positions_atoms[atom_idx] = (new_x, new_y)
+                atom_occupied_sites.add((new_x, new_y))
+    
+                self.time[step + 1] = self.time[step] - (np.log(rho2) / k_tot)
+                    
+                selected_move_name = list(self.moves.keys())[dir_idx]
+                self.selected_moves_info.append((atom_idx, selected_move_name))  # Store the move details
+                move_counts[selected_move_name] += 1
+    
+                displacements = np.sum((self.cumulative_vectors * np.array([self.len_horizontal, self.len_vertical])), axis=1)
+                squared_displacements = np.sum((self.cumulative_vectors * np.array([self.len_horizontal, self.len_vertical])) ** 2, axis=1)
+                
+                k_tot_rec[step] = k_tot 
+                self.md[step] = displacements.mean()
+                self.msd[step] = squared_displacements.mean()
+                
+            return self.time[:-1], self.msd        
+            
+            
+        elif self.defect_type == 2: 
+        
+            for step in range(self.n_steps):
+                            
+                if self.adsorbates_freq != -1:
+                    if step % int(self.adsorbates_freq) == 0:
+                        self.generate_adsorbates()
+                    
+                self.positions_over_time.append(self.positions_atoms.copy())  # Store positions at each step
+                self.positions_adsorbates_over_time.append(self.positions_adsorbates.copy())  # Store hy positions at each step
+                atom_occupied_sites = {tuple(pos) for pos in self.positions_atoms}  # Track occupied sites, position and occupoied sites are the same but different type
+                adsorbates_occupied_sites = {tuple(pos) for pos in self.positions_adsorbates}
+                
+                defects_occ_sites = []
+                for atom_idx, (x, y) in enumerate(self.positions_atoms):
+                    defect = False
+                    for pair in self.defects_pairs:
+                        if (x,y) in pair:
+                            defect = True
+                            break
+                    if defect:
+                       defects_occ_sites.append(pair[0])
+                       defects_occ_sites.append(pair[1])
+                       
+                defects_occupied_sites = {tuple(pos) for pos in defects_occ_sites}
+                
+                total_rate = 0
+                possible_moves = []
+                
+    
+                for atom_idx, (x, y) in enumerate(self.positions_atoms):
+                    
+            
+                        for dir_idx, (dx, dy) in enumerate(list(self.moves.values())):
+                
+                            new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                            new_position = (new_x, new_y)
+                            
+                            if new_position in defects_sites:
+                                 
+                                 if dir_idx == 0:
+                                 
+                                     dx = 3 * dx
+                                     dy = 3 * dy
+                                     new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                                     new_position = (new_x, new_y)
+                                     if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites and (new_x, new_y) not in adsorbates_occupied_sites and (new_x, new_y) not in defects_sites:
+                                         total_rate += list(self.move_rates_blocking_defects.values())[dir_idx]
+                                         possible_moves.append((atom_idx, dir_idx, list(self.move_rates_blocking_defects.values())[dir_idx], (new_x, new_y), dx, dy))    
+                                     
+                                 elif dir_idx == 1:
+                                 
+                                     dx = 3 * dx
+                                     dy = 3 * dy
+                                     new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                                     new_position = (new_x, new_y)
+                                     if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites and (new_x, new_y) not in adsorbates_occupied_sites and (new_x, new_y) not in defects_sites:
+                                         total_rate += list(self.move_rates_blocking_defects.values())[dir_idx]
+                                         possible_moves.append((atom_idx, dir_idx, list(self.move_rates_blocking_defects.values())[dir_idx], (new_x, new_y), dx, dy))    
+                                     
+                                                                   
+                                     
+                                 else:
+                                     dx = 2 * dx
+                                     dy = 2 * dy
+                                     new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                                     new_position = (new_x, new_y)
+                                     if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites and (new_x, new_y) not in adsorbates_occupied_sites and (new_x, new_y) not in defects_sites:
+                                         total_rate += list(self.move_rates_blocking_defects.values())[dir_idx]
+                                         possible_moves.append((atom_idx, dir_idx, list(self.move_rates_blocking_defects.values())[dir_idx], (new_x, new_y), dx, dy))    
+                                     
+                                                 
+         
+                            
+                              
+                            elif new_position in adsorbates_occupied_sites:
+                                
+                                dx = 2 * dx
+                                dy = 2 * dy
+                                new_x, new_y = (x + dx) % self.lattice_size, (y + dy) % self.lattice_size
+                                new_position = (new_x, new_y)
+                                if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites and (new_x, new_y) not in adsorbates_occupied_sites and (new_x, new_y) not in defects_sites:
+                                    total_rate += list(self.move_rates_adsorbates.values())[dir_idx]
+                                    possible_moves.append((atom_idx, dir_idx, list(self.move_rates_adsorbates.values())[dir_idx], (new_x, new_y), dx, dy))    
+                                
+                            else:
+                                
+                                if new_position not in atom_occupied_sites and (new_x, new_y) not in defects_occupied_sites:
+                                    total_rate += list(self.move_rates.values())[dir_idx]
+                                    possible_moves.append((atom_idx, dir_idx, list(self.move_rates.values())[dir_idx], (new_x, new_y), dx, dy))    
+                    
+                rho1, rho2 = np.random.random(), np.random.random()
+    
+                k_tot = total_rate
+                
+                cumulative_rate = 0
+                for move_idx, (atom_idx, dir_idx, rate, new_pos, _, _) in enumerate(possible_moves):
+                    cumulative_rate += rate
+                    if rho1 * k_tot < cumulative_rate:
+                        selected_move = move_idx
+                        break
+                
+                # Execute the selected process
+                 
+                atom_idx, dir_idx, rate, (new_x, new_y), dx, dy = possible_moves[selected_move]
+                
+                if step % int(self.n_steps/10) == 0:
+                    print(f'step = {step}')
+                    
+                # print(f'atom_{atom_idx} moves: dx = {dx}, dy = {dy}')
+                self.cumulative_vectors[atom_idx, 0] += dx
+                self.cumulative_vectors[atom_idx, 1] += dy
+                atom_occupied_sites.remove(self.positions_atoms[atom_idx])
+                self.positions_atoms[atom_idx] = (new_x, new_y)
+                atom_occupied_sites.add((new_x, new_y))
+    
+                self.time[step + 1] = self.time[step] - (np.log(rho2) / k_tot)
+                    
+                selected_move_name = list(self.moves.keys())[dir_idx]
+                self.selected_moves_info.append((atom_idx, selected_move_name))  # Store the move details
+                move_counts[selected_move_name] += 1
+    
+                displacements = np.sum((self.cumulative_vectors * np.array([self.len_horizontal, self.len_vertical])), axis=1)
+                squared_displacements = np.sum((self.cumulative_vectors * np.array([self.len_horizontal, self.len_vertical])) ** 2, axis=1)
+                
+                k_tot_rec[step] = k_tot 
+                self.md[step] = displacements.mean()
+                self.msd[step] = squared_displacements.mean()
+                
+            return self.time[:-1], self.msd
+            
+    def hex_lattice(self):
+        
+        def generate_hexagonal_lattice(rows, cols):
+            hex_lattice = []
+            dx, dy = 1, 1
+
+            for row in range(rows):
+                for col in range(cols):
+                    x = col * dx
+                    y = row * dy
+                    if col % 2 == 1:
+                        y += dy / 2  # Offset every other column
+                    hex_lattice.append((x, y))
+            
+            return hex_lattice
+
+        self.hex_lattice = generate_hexagonal_lattice(self.lattice_size, self.lattice_size)
+        
+    def init_atoms(self):
+        
+        self.positions_atoms = []
+        attempts = 0
+        max_attempts = 1000  # Avoid infinite loops
+
+        while len(self.positions_atoms) < self.n_atoms and attempts < max_attempts:
+            
+            attempts += 1
+            
+            i = np.random.choice(len(self.hex_lattice), replace=False)
+            pos_atom= self.hex_lattice[i]
+            
+            # Check if atom overlaps with an oxygen vacancy (not allowed)
+            if pos_atom in map(tuple, self.positions_defects):
+                continue  # Reject and try again
+            
+            if pos_atom in map(tuple, np.array(self.positions_atoms)):
+                continue  # Reject and try again
+                
+            self.positions_atoms.append(pos_atom)
+
+        self.cumulative_vectors = np.zeros((self.n_atoms, 2), dtype=np.float64)
+        
+    def move_defects(self, pair, lattice_size):
+        x = max(pair, key=lambda x: x[0])[0]
+        mx = max(pair, key=lambda x: x[1])[1]
+        mn = min(pair, key=lambda x: x[1])[1]
+        if mx == lattice_size - 1 and mn == 0:
+            mx = 0   
+            mn = lattice_size - 1
+       
+        new_pos = {
+            "north": ((x), (mx + 1) % lattice_size ),
+            "south": ((x), (mn - 1) % lattice_size),
+            "east": ((x + 1) % lattice_size, (mn + 0.5) % lattice_size),
+            "west": ((x - 1) % lattice_size, (mn + 0.5) % lattice_size),
+            "northeast": ((x + 1) % lattice_size, (mx + 0.5) % lattice_size),
+            "northwest": ((x - 1) % lattice_size, (mx + 0.5) % lattice_size),
+            "southeast": ((x + 1) % lattice_size, (mn - 0.5) % lattice_size),
+            "southwest": ((x - 1) % lattice_size, (mn - 0.5) % lattice_size)
+            
+        }
+       
+        return new_pos
+    
+    def find_pair(self, element, pairs):
+        for pair in pairs:
+            if element == pair[0]:
+                return [pair[0], pair[1]]
+            elif element == pair[1]:
+                return [pair[0] , pair[1]]
+        return None 
+           
+    def generate_defects(self):
+        
+        
+        def is_valid_position(new_pos, existing_positions, lattice_size):
+            """
+            Checks if the new position is valid:
+            - It is not overlapping with an existing position.
+            - It is not a first nearest neighbor of any existing OV.
+            """
+            x, y = new_pos
+            neighbors = [
+                (x % lattice_size, (y + 1)),  # Top
+                (x % lattice_size, (y - 1)),  # Bottom
+                ((x - 1) % lattice_size, (y + 0.5) % lattice_size),  #nw
+                ((x + 1) % lattice_size, (y + 0.5) % lattice_size),   #ne
+                ((x - 1) % lattice_size, (y - 0.5) % lattice_size), #sw
+                ((x + 1) % lattice_size, (y - 0.5) % lattice_size),  #se
+                (x % lattice_size, (y + 2)),  # Top
+                (x % lattice_size, (y - 2)),  # Bottom
+                ((x + 1) % lattice_size, (y + 1.5) % lattice_size),  #ne
+                ((x + 1) % lattice_size, (y - 1.5) % lattice_size),   #nw
+                ((x - 1) % lattice_size, (y - 1.5) % lattice_size), #sw
+                ((x - 1) % lattice_size, (y + 1.5) % lattice_size)  #se
+            ]
+            
+            return tuple(new_pos) not in existing_positions and all(tuple(pos) not in existing_positions for pos in neighbors)
+
+        def defects(lattice_size, n_defects):
+            max_possible_sites = lattice_size * lattice_size // 6  # Allow more vacancies
+            if n_defects > max_possible_sites:
+                raise ValueError(f"n_defects ({n_defects}) is too large for lattice_size={lattice_size}!")
+
+            if n_defects == 0:  
+                return np.empty((0, 2), dtype=int)  # Return an empty 2D array when no vacancies are needed
+
+            positions_base_defects = set()
+            attempts = 0
+            max_attempts = 20000  # Allow more attempts to fit more vacancies
+            
+            y_values_even = np.arange(0, lattice_size -1, 1)
+            y_values_odd = np.arange(0.5, lattice_size - 0.5, 1)
+            
+            while len(positions_base_defects) < n_defects and attempts < max_attempts:
+                x = np.random.randint(0, lattice_size)
+                if x % 2 ==0:
+                    y = np.random.choice(y_values_even)
+                    new_pos = (x, y)
+                else:
+                    
+                    y = np.random.choice(y_values_odd)
+                    new_pos = (x, y)
+                    
+                if is_valid_position(new_pos, positions_base_defects, lattice_size):
+                    positions_base_defects.add(new_pos)
+
+                attempts += 1
+
+            if len(positions_base_defects) < n_defects:
+                raise RuntimeError("Could not place all vdefects while avoiding overlaps and first-nearest neighbors.")
+
+            positions_base_defects = np.array(list(positions_base_defects))
+            
+            # Compute the "above" positions (shifted by one row up)
+            positions_above_defects = np.column_stack((positions_base_defects[:, 0], ((positions_base_defects[:, 1] + 1) % lattice_size)))
+            
+            # Combine base and above positions
+            positions_defects = np.vstack((positions_base_defects, positions_above_defects))
+
+            return positions_defects
+
+        self.positions_defects = defects(self.lattice_size, self.n_defects)
+
+        arr = self.positions_defects
+        self.defects_pairs = [[tuple(arr[j]), tuple(arr[int(j + 0.5 * len(arr))])] for j in range(int(0.5 * len(arr)))]
+    
+    def generate_adsorbates(self):
+        
+        self.positions_adsorbates = []
+        attempts = 0
+        max_attempts = 1000  # Avoid infinite loops
+
+        while len(self.positions_adsorbates) < self.n_adsorbates and attempts < max_attempts:
+            
+            # print(f'attempt = {attempts}')
+            attempts += 1
+            
+            i = np.random.choice(len(self.hex_lattice), replace=False)
+            pos_adsorbates= self.hex_lattice[i]
+            
+            # Check if hydroxyl overlaps with an oxygen vacancy (not allowed)
+            if pos_adsorbates in map(tuple, self.positions_defects) or pos_adsorbates in map(tuple, self.positions_atoms):
+                continue  # Reject and try again
+            
+
+            # If all conditions are met, accept the position
+            self.positions_adsorbates.append(pos_adsorbates)
+
+        self.positions_adsorbates = np.array(self.positions_adsorbates)
+    
+
+    
+ 
+    
+    def anim1panels(self, filename):
+
+    
+        # ===================== Figure & Axes =====================
+        fig, ax_main = plt.subplots(figsize=(6, 6))
+        ax_main.set_xlim(-1, self.lattice_size + 1)
+        ax_main.set_ylim(-1, self.lattice_size + 1)
+        ax_main.set_xticks(range(self.lattice_size))
+        ax_main.set_yticks(range(self.lattice_size))
+        ax_main.grid(True, linestyle='--', linewidth=0.5)
+        ax_main.set_aspect('equal', adjustable='box')  # ensure circles look like circles
+    
+        # Background lattice (optional)
+        if hasattr(self, "hex_lattice") and len(self.hex_lattice) > 0:
+            hx, hy = zip(*self.hex_lattice)
+            ax_main.scatter(hx, hy, s=20, color="gray", alpha=0.5, label="Lattice Sites")
+    
+        title_text = ax_main.set_title("")
+    
+        # ===================== OV Rectangles =====================
+        if hasattr(self, "defects_pairs") and self.defects_pairs:
+            for defect1, defect2 in self.defects_pairs:
+                x_min = min(defect1[0], defect2[0])
+                y_min = min(defect1[1], defect2[1])
+                if defect1[1] == defect2[1]:      # horizontal
+                    width, height = abs(defect1[0] - defect2[0]) + 1, 1
+                elif defect1[0] == defect2[0]:    # vertical
+                    width, height = 1, abs(defect1[1] - defect2[1]) + 1
+                else:                     # diagonal/block
+                    width  = abs(defect1[0] - defect2[0]) + 1
+                    height = abs(defect1[1] - defect2[1]) + 1
+    
+                rect = patches.Rectangle(
+                    (x_min - 0.5, y_min - 0.5), width, height,
+                    edgecolor='darkgray', facecolor=(245/255, 245/255, 245/255, 0.4), linewidth=2, zorder=3
+                )
+                ax_main.add_patch(rect)
+    
+        # ===================== Hydroxyls (dynamic) =====================
+        adsorbates_circles = []
+        if hasattr(self, "positions_adsorbates_over_time") and len(self.positions_adsorbates_over_time) > 0:
+            adsorbates_n = len(self.positions_adsorbates_over_time[0])
+            for _ in range(adsorbates_n):
+                c = patches.Circle((0, 0),  edgecolor='dimgray', radius=0.2, color='darkred', alpha=0.95, zorder=9)
+                ax_main.add_patch(c)
+                adsorbates_circles.append(c)
+    
+        # ===================== Atom Gradient Setup =====================
+        # Baby blue gradient: bright center -> slightly darker edge
+        # Lightsteelblue gradient: center almost white → edge lightsteelblue
+        center_color = np.array([240/255, 245/255, 250/255, 1.0])  # very light (near white)
+        edge_color   = np.array([176/255, 196/255, 222/255, 1.0])  #
+    
+        def radial_gradient_image(resolution=256):
+            y, x = np.ogrid[-1:1:complex(0, resolution), -1:1:complex(0, resolution)]
+            r = np.sqrt(x*x + y*y)
+            r = np.clip(r, 0, 1)
+            grad = (1 - r)[..., None] * center_color + r[..., None] * edge_color  # (H,W,4)
+            return grad.astype(float)
+    
+        grad_img = radial_gradient_image(256)
+    
+        atom_radius = 0.25
+        outline_color = 'midnightblue'
+        outline_width = 1.5
+    
+        # Create atom visuals: (circle outline + clipped gradient image) per atom
+        atom_artists = []  # list of (circle_patch, image_artist)
+        for _ in range(self.n_atoms):
+            # Circle outline (above the gradient)
+            circle = patches.Circle(
+                (0, 0), radius=atom_radius,
+                edgecolor=outline_color, facecolor='none',
+                linewidth=outline_width, zorder=7
+            )
+            ax_main.add_patch(circle)
+    
+            # Gradient image (under the outline), then clip to the circle
+            im = ax_main.imshow(
+                grad_img,
+                extent=[-atom_radius, atom_radius, -atom_radius, atom_radius],
+                origin='lower',
+                interpolation='bilinear',
+                zorder=6,
+                alpha=1.0
+            )
+            im.set_clip_path(circle)  # critical: clip the image to the circle
+            im.set_clip_on(True)
+    
+            atom_artists.append((circle, im))
+    
+        # Transparent numbers centered inside atoms
+        labels = [
+            ax_main.text(
+                0, 0, str(i),
+                fontsize=6, color='black',
+                ha='center', va='center',
+                fontweight='bold', alpha=1,
+                zorder=8
+            )
+            for i in range(self.n_atoms)
+        ]
+    
+        # ===================== Update Function =====================
+        def update(frame):
+            # Move atoms
+            for i, (circle, im) in enumerate(atom_artists):
+                x, y = self.positions_over_time[frame][i]
+                circle.center = (x, y)
+                im.set_extent([x - atom_radius, x + atom_radius, y - atom_radius, y + atom_radius])
+                # (re)set clip path (safe across some backends)
+                im.set_clip_path(circle)
+                labels[i].set_position((x, y))
+    
+            # Title
+            if hasattr(self, "selected_moves_info") and frame < len(self.selected_moves_info):
+                atom_idx, move_name = self.selected_moves_info[frame]
+                title_text.set_text(f"next: selected atom is atom_{atom_idx} and selected move is {move_name}")
+            else:
+                title_text.set_text("")
+    
+            # Move hydroxyls
+            if adsorbates_circles:
+                for i, pos in enumerate(self.positions_adsorbates_over_time[frame]):
+                    adsorbates_circles[i].center = (pos[0], pos[1])
+    
+        # ===================== Animate (pause on last frame) =====================
+        interval_ms = 100
+        pause_frames = int(10_000 / interval_ms)  # 10 sec
+        def update_with_pause(frame):
+            if frame < self.n_steps:
+                update(frame)
+            else:
+                update(self.n_steps - 1)
+    
+        ani = FuncAnimation(fig, update_with_pause, frames=self.n_steps + pause_frames, interval=interval_ms)
+        ani.save(f"{filename}.gif", writer=PillowWriter(fps=20))
+        plt.show()
+
+
+
+    
+        
+    def anim2panels(self, filename):
+
+        fig, axes = plt.subplots(1, 2, figsize=(12, 6), gridspec_kw={'width_ratios': [2, 1]})
+        ax_main, ax_msd = axes[0], axes[1]
+    
+        # ---- Main lattice view ----
+        ax_main.set_xlim(-1, self.lattice_size + 1)
+        ax_main.set_ylim(-1, self.lattice_size + 1)
+        ax_main.set_xticks(range(self.lattice_size))
+        ax_main.set_yticks(range(self.lattice_size))
+        ax_main.grid(True, linestyle='--', linewidth=0.5)
+        ax_main.set_aspect('equal', adjustable='box')  # keep circles round
+    
+        if hasattr(self, "hex_lattice") and len(self.hex_lattice) > 0:
+            hex_x, hex_y = zip(*self.hex_lattice)
+            ax_main.scatter(hex_x, hex_y, s=20, color="gray", alpha=0.5, label="Lattice Sites")
+    
+        title_text = ax_main.set_title("")
+    
+        # ---- OV rectangles: whitesmoke fill with adjustable transparency ----
+        defect_alpha = 0.4  # <— tweak this for more/less transparent OV fill
+        if hasattr(self, "defects_pairs"):
+            for defect1, defect2 in self.defects_pairs:
+                x_min = min(defect1[0], defect2[0])
+                y_min = min(defect1[1], defect2[1])
+    
+                if defect1[1] == defect2[1]:  # Horizontal pair
+                    width, height = abs(defect1[0] - defect2[0]) + 1, 1
+                elif defect1[0] == defect2[0]:  # Vertical pair
+                    width, height = 1, abs(defect1[1] - defect2[1]) + 1
+                else:
+                    width  = abs(defect1[0] - defect2[0]) + 1
+                    height = abs(defect1[1] - defect2[1]) + 1
+    
+                rectangle = patches.Rectangle(
+                    (x_min - 0.5, y_min - 0.5), width, height,
+                    edgecolor='gray',
+                    facecolor='whitesmoke',
+                    linewidth=1.5,
+                    alpha=defect_alpha,
+                    zorder=3
+                )
+                ax_main.add_patch(rectangle)
+    
+        # ---- Hydroxyls (dynamic small red circles) ----
+        adsorbates_circles = []
+        if hasattr(self, "positions_adsorbates_over_time") and len(self.positions_adsorbates_over_time) > 0:
+            for _ in range(len(self.positions_adsorbates_over_time[0])):
+                c = patches.Circle((0, 0), linewidth=2.5, edgecolor='dimgray', radius=0.2, color='darkred', alpha=0.9, zorder=9)
+                ax_main.add_patch(c)
+                adsorbates_circles.append(c)
+    
+        # ---- Atoms: lightsteelblue radial gradient + gray outline ----
+        # Gradient colors: center almost white -> edge lightsteelblue
+        center_color = np.array([240/255, 245/255, 250/255, 1.0])  # near white
+        edge_color   = np.array([176/255, 196/255, 222/255, 1.0])  # lightsteelblue (#B0C4DE)
+    
+        def radial_gradient_image(resolution=256):
+            y, x = np.ogrid[-1:1:complex(0, resolution), -1:1:complex(0, resolution)]
+            r = np.sqrt(x*x + y*y)
+            r = np.clip(r, 0, 1)
+            grad = (1 - r)[..., None] * center_color + r[..., None] * edge_color  # (H,W,4)
+            return grad.astype(float)
+    
+        grad_img = radial_gradient_image(256)
+        atom_radius = 0.25
+        outline_color = 'midnightblue'
+        outline_width = 1.5
+    
+        # Create per-atom (circle outline + clipped gradient image)
+        atom_artists = []  # list of (circle_patch, image_artist)
+        for _ in range(self.n_atoms):
+            circle = patches.Circle(
+                (0, 0), radius=atom_radius,
+                edgecolor=outline_color, facecolor='none',
+                linewidth=outline_width, zorder=7
+            )
+            ax_main.add_patch(circle)
+    
+            im = ax_main.imshow(
+                grad_img,
+                extent=[-atom_radius, atom_radius, -atom_radius, atom_radius],
+                origin='lower',
+                interpolation='bilinear',
+                zorder=6,
+                alpha=1.0
+            )
+            im.set_clip_path(circle)  # clip gradient to the circle
+            im.set_clip_on(True)
+    
+            atom_artists.append((circle, im))
+    
+        # Atom labels: centered, semi-transparent
+        labels = [
+            ax_main.text(
+                0, 0, str(i),
+                fontsize=6, color='black',
+                ha='center', va='center',
+                fontweight='bold', alpha=1,
+                zorder=8
+            )
+            for i in range(self.n_atoms)
+        ]
+    
+        # ---- MSD plot setup ----
+        ax_msd.set_xlim(0, np.max(self.time) * 1.1)
+        ax_msd.set_ylim(0, np.max(self.msd) * 1.1)
+        ax_msd.set_xlabel("time (s)")
+        ax_msd.set_ylabel("MSD (µm²)")
+        ax_msd.grid(True, linestyle='--', linewidth=0.5)
+    
+        (msd_line,) = ax_msd.plot([], [], color="#FFB6C1", label="MSD")
+        (fit_line,) = ax_msd.plot([], [], linestyle='--', color='midnightblue', label="Linear Fit")
+        slope_text = ax_msd.text(0.05, 0.1, "", transform=ax_msd.transAxes, fontsize=8, ha="left", va="top")
+    
+        ax_msd.set_title("MSD over time")
+        ax_msd.legend()
+    
+        # ---- Move stats (percentages) ----
+        move_labels = list(self.moves.keys())
+        move_texts = []
+        for i, move in enumerate(move_labels):
+            text = ax_msd.text(
+                0.5, 0.9 - i * 0.1,
+                f"{move}: 0%",
+                transform=ax_msd.transAxes,
+                fontsize=10, ha="center", va="top"
+            )
+            move_texts.append(text)
+    
+        # ---- Frame update ----
+        def update(frame):
+            # Atoms
+            for i, (circle, im) in enumerate(atom_artists):
+                x, y = self.positions_over_time[frame][i]
+                circle.center = (x, y)
+                im.set_extent([x - atom_radius, x + atom_radius, y - atom_radius, y + atom_radius])
+                im.set_clip_path(circle)  # safe across backends
+                labels[i].set_position((x, y))
+    
+            # Title
+            atom_idx, selected_move_name = self.selected_moves_info[frame]
+            title_text.set_text(f"next: selected atom is atom_{atom_idx} and selected move is {selected_move_name}")
+    
+            # Hydroxyls
+            for i, pos in enumerate(self.positions_adsorbates_over_time[frame]):
+                adsorbates_circles[i].center = (pos[0], pos[1])
+    
+            # MSD trace
+            msd_line.set_data(self.time[:frame], self.msd[:frame])
+    
+            # Move percentages up to current frame
+            move_counts_up_to_frame = {m: 0 for m in move_labels}
+            for _, mname in self.selected_moves_info[:frame]:
+                move_counts_up_to_frame[mname] += 1
+            total_moves = max(1, sum(move_counts_up_to_frame.values()))
+            for i, m in enumerate(move_labels):
+                pct = 100.0 * move_counts_up_to_frame[m] / total_moves
+                move_texts[i].set_text(f"{m}: {pct:.1f}%")
+    
+            # Linear fit for diffusion slope
+            if frame > 1:
+                x_fit = self.time[:frame]
+                y_fit = self.msd[:frame]
+                p = Polynomial.fit(x_fit, y_fit, 1).convert()
+                slope = p.coef[1]
+                fit_line.set_data(x_fit, p(x_fit))
+                slope_text.set_text(f"Diffusion = {slope/4:.3f}(µm²/s)")
+            else:
+                fit_line.set_data([], [])
+                slope_text.set_text("")
+    
+        # ---- Animate with pause at end ----
+        interval_ms = 100
+        pause_frames = int(10_000 / interval_ms)  # 10 sec hold
+        def update_with_pause(frame):
+            if frame < self.n_steps:
+                update(frame)
+            else:
+                update(self.n_steps - 1)
+    
+        ani = FuncAnimation(fig, update_with_pause, frames=self.n_steps + pause_frames, interval=interval_ms)
+        ani.save(f"{filename}.gif", writer=PillowWriter(fps=20))
+        plt.show()
+        
+        
+        
+       
+    def msdplot(self, filename):
+        
+        time = self.time[:-1]
+
+        ## Calculate overall diffusion coefficient
+        transient_cutoff = int(0 * self.n_steps)  # Ignore the first 10% of steps
+        valid_time = time[transient_cutoff:]  # Exclude transient region
+        valid_msd = self.msd[transient_cutoff:]    # Exclude transient region
+
+        # Linear fit for MSD vs time
+        fit = Polynomial.fit(valid_time, valid_msd, 1).convert()
+        fit_line = fit(valid_time)
+        average_slope = fit.coef[1]  # Slope of MSD vs time
+
+        # Diffusion coefficient
+        diffusion_coefficient_corrected = average_slope / 4
+
+        # Plot MSD vs. time with fit line
+        plt.figure(figsize=(8, 6))
+        plt.plot(time, self.msd,  color="#89CFF0", label="Individual MSD Trajectory")
+        plt.plot(valid_time, fit_line, linestyle="--", color="blue", label="Linear Fit")
+        #plt.axvline(x=time[transient_cutoff], color='r', linestyle='--', label="Transient cutoff")
+        plt.xlabel("Time (s)")
+        plt.ylabel("MSD (µm²)")
+        plt.legend()
+        plt.title(f"Mean Squared Displacement vs Time - {self.n_steps} steps")
+        plt.text(0.05 * max(time), 0.8 * max(self.msd),  # Adjust placement (x, y) as needed
+                 f" Diffusion Coefficient = {diffusion_coefficient_corrected:.4f} µm²/s", 
+                 fontsize=12, color='blue', bbox=dict(facecolor="white", alpha=0.5))
+        plt.minorticks_on()
+        plt.grid(True, which='major', linestyle='-', linewidth=0.6)
+        plt.grid(True, which='minor', linestyle=':', linewidth=0.3, alpha=0.7)
+        plt.savefig(f'{filename}.png', dpi = 600)
+        plt.show()  
+        
+        
+
+    def msd_histogram(self, n_seeds, msd_folder = "random_seeds/msd", 
+                      time_folder = "random_seeds/time", 
+                      save_folder = "random_seeds/average_msd.png",
+                      msd_trajs_color = "pink",
+                      msd_average_color = "#C71585"):
+        
+        
+        msd_list = []
+        time_list = []
+
+        for i in range(n_seeds):
+            msd = np.load(f"{msd_folder}/rs_{i}.npy")
+            time = np.load(f"{time_folder}/rs_{i}.npy")
+            msd_list.append(msd)
+            time_list.append(time)
+
+        # Convert lists to numpy arrays
+        msd_array = np.array(msd_list) 
+        time_array = np.array(time_list)
+
+        # Compute average and standard deviation
+        msd_avg = np.mean(msd_array, axis=0)
+        msd_std = np.std(msd_array, axis=0)
+        time_avg = np.mean(time_array, axis=0)
+
+        # Fit a linear function: MSD = a * Time + b
+       # slope, intercept = np.polyfit(time_avg, msd_avg, 1)
+        slope, intercept, r_value, p_value, slope_std_err = linregress(time_avg, msd_avg)
+        fitted_line = slope * time_avg + intercept  # Compute the fitted line
+
+        # Select 20 evenly spaced points for error bars
+        num_error_points = 20
+        indices = np.linspace(0, len(time_avg) - 1, num_error_points, dtype=int)
+
+        # Plot all MSD curves in light pink
+        plt.figure(figsize=(8, 6))
+        for i in range(n_seeds):
+            plt.plot(time_array[i], msd_array[i], color=msd_trajs_color, alpha=0.5, linewidth=1)
+
+        # Plot average MSD with error bars at 20 selected points in dark pink
+        plt.plot(time_avg, msd_avg, color=msd_average_color, linewidth=2, label="Average MSD")
+        plt.errorbar(time_avg[indices], msd_avg[indices], yerr=msd_std[indices], fmt='o', color=msd_average_color, capsize=3)
+
+        # Plot fitted line
+        #plt.plot(time_avg, fitted_line, linestyle="--", color="blue", linewidth=2, label=f"Linear Fit: Slope = {slope:.4f} ± {slope_std_err:.2f} (um²/s)")
+        plt.plot(time_avg, fitted_line, linestyle="--", color="blue", linewidth=2, label="Linear Fit")
+
+        # Labels and legend
+        plt.xlabel("Time(s)")
+        plt.ylabel("MSD (µm²)")
+        plt.title("T=300K - Lattice Size =10*10 - OH Coverage=0.5ML - OH Frequency=OFF")
+
+        # Display slope inside the plot
+        plt.text(0.05 * max(time_avg), 0.8 * max(msd_avg), f"Diffusion Coefficient = {slope/4:.6f} ± {slope_std_err/4:.1e} (µm²/s)", fontsize=12, color="blue", bbox=dict(facecolor="white", alpha=0.5))
+        plt.legend()
+        plt.minorticks_on()
+        plt.grid(True, which='major', linestyle='-', linewidth=0.6)
+        plt.grid(True, which='minor', linestyle=':', linewidth=0.3, alpha=0.7)
+        plt.savefig(save_folder, dpi = 600)
+        plt.show()
+    
+