[QE-users] Question about NEB

[Yeon, Jejoon]

Hello

I'm attempting to calculate Mg ion vacancy migration inside Pyrope unit cell. System has total 159 atoms, beginning and end geometry is optimized. I attached input file in this email. For intermediate image, I'm using one coordinate that I acquired from crashed NEB case. This is not perfect intermediate geometry, but I thought this should be enough one to guide NEB.

1) Is there any rule of thumb to decide "num_of_images" based on moving distance of target atom?
In my script, I wish to move one Mg atom (atom ID 4) from one position to next vacancy which is about 3.5 angstrom away. For example, if I choose 1 image per 0.5 angstrom, then 8 images should be chosen including the beginning and the end. But I'm not sure if 1 image per 0.5 angstrom would be the proper value. How do you decide "num_of_images" per given distance?

2) How many core number should be chosen for NEB?
I have some sense of core number decision based on my experience, but this is for relaxation. For NEB, I'm not sure how much core number is proper for given atom number or given num_of_images setting. As we all know, QE can make crash because of too much memory or too low memory, I wish to learn if there are rule of thumb to decide core number for given NEB conditions.

3) How to decide intermediate image?
First, I tried my best guess of Mg ion (atom ID 4) between two vacancies as an intermediate iamge. Then, I'm using one from one of the crashed NEB simulation result. Is this good judge?

4) Can freezing atom helps convergence?
Is this better to freeze (put 1 1 1 beside the atom coordinate) the target atom for the beginning, intermediate, and end geometry? Or surrounding atoms? For now I'm not inducing any freeze to any atom in my NEB setting, but I'm curious if freezing helps convergence of NEB calculation.

5) How can I escape from segmentation fault error?
My setting is experiencing segmentation fault error. I'm testing my setting by varying some conditions, but I couldn't escape from seg fault error. I know seg fault can happen from so many possibilities, but I wish to learn if there are any checklist to solve seg fault error during NEB from other researchers.

Thank you


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