UT theoretical chemistry code forum

Oh, I see what you mean! I should have realized that.
Thank you so much, sir, for your patience and help! :)

Thank you, Prof. Henkelman, for your prompt response!

Just to clarify, when you mentioned it’s best to download all the vtstscripts and run them from a single directory, which directory are you referring to?

Should I place nebmovie.pl, pos2con.pl, and con2xyz.pl in each image directory, or is it ...

Hello everyone,

I have completed my NEB calculations and now want to generate a movie. I found a brief description of the `nebmovie.pl` script on the webpage and followed the instructions. I made sure to enable all necessary flags in the script:


$xdatflag = 1; # Enable XDATCAR writing
$xyzflag ...

Dr. Henkelman,

I restarted the calculation by copying the CONTCAR of all images (from the 869th iteration) as the new POSCAR files for each image and the job successfully finished in about an hour. However, this is what I got in the neb.dat file:
0 0.000000 0.000000 0.000000 0
1 2.256204 0.075494 ...

Indeed, it’s puzzling. I’m just wondering, since it’s been three days and the job is still running without any new updates, should I just let it continue or do something else? Thank you for the help :)

The issue is that the job is still running, but it is not updating the stdout file. I have just uploaded the stderr and stdout files to the link you provided.

Can I upload those stdout files for your review?

Just did it. I have uploaded the other one as well. Thank you so much for your help :)

I can only upload one file on the link you provide (90086.tar.gz- Interstitial Diffusion), which is 456 MB in size. The other file is 4.26 GB, and I believe I cannot upload it due to the storage limitation (maximum limit of 500 MB). However, I have already emailed that file (90232.tar.gz-Vacancy ...

Thank you so much for the reply. I have already emailed it to you; however, I can also share it through the other option you provided.

Can I email it to you? I need to maintain the confidentiality of my data.
Thank you!

Hello Dr. Henkelman,

I’m running NEB calculations using VASP for interstitial diffusion, but my job seems to be stuck at the 84th iteration. There are no error messages or issues in the output files, and the job is still running, but it’s not progressing. I am using 2 nodes with a total of 60 ...

Hello Dr. Henkelman,

Update:

When I first ran the nebresult.pl script, it generated various files, and this time I noticed that the neb.dat file was updated with the following data:

0 0.000000 0.000000 0.000000 0
1 19.846714 -12.324307 0.522118 1
2 39.643102 -10.626521 -2.124996 2
3 59.645364 1 ...

Hello Dr. Henkelman,

I’ve just started my NEB calculations. Initially, when I used the nebmake.pl script to generate 5 images, I found that in two images, some ions were overlapping. I then used the nebavoid.pl script, and the issue was resolved.

Now, I have a question regarding the following:

1 ...

Thank you so much, Dr. Henkleman. I understand what you are referring to, but I feel that if you and Dr. Wheat, my HPC administrator, can connect, we can work through the setup together. I'll send you an email and will copy Dr. Wheat on it. I really want to get this resolved, as I find your NEB ...