init

neb.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+"""
+NEB path generator for VASP
+Usage: python neb.py -n 5 00/POSCAR 0N/POSCAR
+"""
+
+import numpy as np
+import os
+import sys
+import argparse
+from ase import Atoms
+from ase.io import read, write
+from ase.neb import NEB
+from ase.calculators.vasp import Vasp
+
+def create_interpolated_images(initial, final, n_images):
+    """Create NEB images between initial and final structures"""
+    images = [initial]
+    
+    # Create intermediate images
+    for i in range(1, n_images):
+        image = initial.copy()
+        # Linear interpolation
+        image.positions = initial.positions + i/(n_images+1) * (final.positions - initial.positions)
+        images.append(image)
+    
+    images.append(final)
+    
+    # Create NEB object for interpolation
+    neb = NEB(images)
+    neb.interpolate()
+    
+    return images
+
+def main():
+    parser = argparse.ArgumentParser(description='Generate NEB images for VASP')
+    parser.add_argument('-n', '--n_images', type=int, default=3,
+                       help='Number of intermediate images')
+    parser.add_argument('initial_poscar', help='Path to initial POSCAR')
+    parser.add_argument('final_poscar', help='Path to final POSCAR')
+    parser.add_argument('--method', default='idpp',
+                       help='Interpolation method (idpp or linear)')
+    
+    args = parser.parse_args()
+    
+    # Read structures
+    initial = read(args.initial_poscar, format='vasp')
+    final = read(args.final_poscar, format='vasp')
+    
+    print(f"Initial structure: {len(initial)} atoms")
+    print(f"Final structure: {len(final)} atoms")
+    
+    # Check atom count
+    if len(initial) != len(final):
+        print("ERROR: Initial and final structures must have same number of atoms!")
+        sys.exit(1)
+    
+    # Create images
+    images = create_interpolated_images(initial, final, args.n_images)
+    
+    # Create directories and write POSCAR files
+    for i, image in enumerate(images):
+        dir_name = f"{i:02d}"
+        os.makedirs(dir_name, exist_ok=True)
+        write(f"{dir_name}/POSCAR", image, format='vasp', direct=True)
+        print(f"Created {dir_name}/POSCAR")
+    
+    # Write NEB information
+    with open('NEB_INFO.txt', 'w') as f:
+        f.write(f"NEB calculation with {len(images)} images\n")
+        f.write(f"Initial: {args.initial_poscar}\n")
+        f.write(f"Final: {args.final_poscar}\n")
+        f.write(f"Intermediate images: {args.n_images}\n")
+    
+    print(f"\nCreated {len(images)} images in directories 00-{len(images)-1:02d}")
+    print("Next steps:")
+    print("1. Copy INCAR, KPOINTS, POTCAR to all image directories")
+    print("2. Run VASP in the main directory")
+    print("3. Check convergence in OUTCAR files")
+
+if __name__ == '__main__':
+    main()