NEB Calculation

[sulee]

Dear Sir/Madam,

I have tried to use NEB input generator.
I want to calculate oxygen diffusion energy barrier.
But, the generated images have so many ionic rearrangement, even though I expect only one oxygen movement.
Please find the attached files.

Please let me know how can I generate proper NEB image structures.

Best regards,

Sang Uck Lee

[Jess Wellendorff]

The NEB Builder will detect which atoms in the initial and final states have different positions. If you run the attached script in the folder where you have the Initial.nc and Final.nc data files, you will see that several of your oxygen atoms have different coordinates in the initial and final states, see output below. I think several oxygen atoms end up swapping positions. That is the problem you need to fix.

32 Oxygen [ 0.  0.  0.]
33 Oxygen [-3.7842  3.7842  0.    ]
34 Oxygen [ 0.     -3.7842  0.    ]
35 Oxygen [ 3.7842   5.6763  -2.37865]
36 Oxygen [ 0.     -3.7842  0.    ]
37 Oxygen [-3.7842  3.7842  0.    ]
38 Oxygen [ 0.     -3.7842  0.    ]
39 Oxygen [ 3.7842      1.8921      6.33862652]
40 Oxygen [ 0.     -3.7842  0.    ]
41 Oxygen [-3.7842  3.7842  0.    ]
42 Oxygen [ 0.     -3.7842  0.    ]
43 Oxygen [ 3.7842   5.6763  -2.37865]
44 Oxygen [ 0.     -3.7842  0.    ]
45 Oxygen [ 0.  0.  0.]
46 Oxygen [ 0.  0.  0.]

[Jess Wellendorff]

To elaborate: Each atom in a bulk configuration is assigned an index. The NEB Builder creates the NEB path by moving the atom with index X from initial to final coordinates. Therefore, it is recommended to create the final state from the initial one (by moving the atom(s) that should diffuse).