NEB in pymatgen

[ghost]

Hi all,

I am new to pymatgen. Can anyone please help me with how to obtain the distinct hopping path and corresponding their initial and final structure from the NEB module? I would be really grateful if anyone kindly help.

Thank you!

[shyuep]

The module in pymatgen itself is defunct. Pls use the pymatgen-analysis-diffusion add-on.

[ghost]

Hi,

NEB get_structure results in wrong structures.

import os
import shutil
from pymatgen.core import Structure
from pymatgen.analysis.diffusion.neb.pathfinder import DistinctPathFinder

# Step 1: Read the structure from the file
s = Structure.from_file("st_opt.vasp")

# Step 2: Find the distinct migration paths for the specified specie
migrating_specie = "Na"  # Replace this with the migrating species
max_path_length = 6.0  # Maximum length of NEB path in Angstroms

path_finder = DistinctPathFinder(s, migrating_specie, max_path_length=max_path_length)

# Step 3: Obtain all distinct migration paths
paths = path_finder.get_paths()

print("Path\tMigration Hop Distance (Å)")
for i, p in enumerate(paths):
    migration_distance = p.length
    print(f" {i+1}\t{migration_distance:.4f}")
    # Step 4: Generate path visual

output_dir = "migration_paths"
if os.path.exists(output_dir):
    shutil.rmtree(output_dir)

# Create a new directory to save the structures
os.makedirs(output_dir)

nimages = 5  # Number of images per path

for i, p in enumerate(paths):
    p_dir = os.path.join(output_dir, f"path_{i}")
    os.makedirs(p_dir, exist_ok=True)    
    st = p.get_structures(nimages=nimages, vac_mode=False, idpp=False)
    st[0].to(filename=os.path.join(p_dir, "ini.cif"))
    st[-1].to(filename=os.path.join(p_dir, "fin.cif"))
```
`
It is giving me wrong  ini.cif  and fin.cif structures, which has lesser migrating ions as initial given in st_opt.vasp file