init

analyze_neb.py

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+#!/usr/bin/env python3
+"""
+Analyze NEB results and calculate reaction rate
+"""
+
+import numpy as np
+import os
+import matplotlib.pyplot as plt
+from ase.io import read
+from ase.neb import NEBTools
+
+def read_neb_energies():
+    """Read energies from OUTCAR files"""
+    energies = []
+    forces = []
+    
+    # Find all image directories
+    dirs = sorted([d for d in os.listdir('.') if os.path.isdir(d) and d.isdigit()])
+    
+    for d in dirs:
+        outcar = os.path.join(d, 'OUTCAR')
+        if os.path.exists(outcar):
+            with open(outcar, 'r') as f:
+                lines = f.readlines()
+                for line in lines:
+                    if 'free  energy   TOTEN' in line:
+                        energy = float(line.split()[-2])
+                        energies.append(energy)
+                    elif 'TOTAL-FORCE' in line:
+                        # Read forces (simplified)
+                        pass
+    
+    return np.array(energies)
+
+def calculate_reaction_rate(E_a, T=300, A=1e13):
+    """
+    Calculate reaction rate using Arrhenius equation
+    k = A * exp(-E_a / (k_B * T))
+    
+    Parameters:
+    E_a: activation energy (eV)
+    T: temperature (K)
+    A: pre-exponential factor (s^-1)
+    
+    Returns:
+    k: reaction rate (s^-1)
+    """
+    k_B = 8.617333262145e-5  # eV/K
+    k = A * np.exp(-E_a / (k_B * T))
+    return k
+
+def main():
+    # Read energies
+    energies = read_neb_energies()
+    
+    if len(energies) == 0:
+        print("No OUTCAR files found!")
+        return
+    
+    print(f"Found {len(energies)} images")
+    print(f"Energies (eV): {energies}")
+    
+    # Calculate activation energy
+    E_a = energies.max() - energies[0]
+    print(f"\nActivation energy E_a = {E_a:.3f} eV")
+    
+    # Calculate reaction rates at different temperatures
+    temperatures = [250, 300, 350, 400, 450, 500]
+    print("\nReaction rates (s^-1):")
+    for T in temperatures:
+        k = calculate_reaction_rate(E_a, T)
+        print(f"T = {T} K: k = {k:.2e} s^-1")
+    
+    # Plot energy profile
+    plt.figure(figsize=(10, 6))
+    plt.plot(range(len(energies)), energies - energies[0], 'o-', linewidth=2)
+    plt.xlabel('Reaction coordinate (image number)')
+    plt.ylabel('Energy (eV)')
+    plt.title(f'NEB Energy Profile (E_a = {E_a:.3f} eV)')
+    plt.grid(True, alpha=0.3)
+    plt.savefig('neb_energy_profile.png', dpi=300)
+    plt.show()
+    
+    # Save results
+    with open('neb_results.txt', 'w') as f:
+        f.write(f"Activation energy: {E_a:.6f} eV\n")
+        f.write(f"Energy barrier: {energies.max() - energies.min():.6f} eV\n")
+        f.write(f"Reaction energy: {energies[-1] - energies[0]:.6f} eV\n")
+        f.write("\nReaction rates:\n")
+        for T in temperatures:
+            k = calculate_reaction_rate(E_a, T)
+            f.write(f"T = {T} K: k = {k:.6e} s^-1\n")
+
+if __name__ == '__main__':
+    main()