nebmake.pl bug?

Vasp transition state theory tools

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kai
Posts: 55
Joined: Sun Oct 31, 2010 11:01 pm

nebmake.pl bug?

Post by kai »

Hi, everyone,

I have been using nebmake.pl to prepare my files, and everything went on fine until recently. Simply put, nebmake didnt interpolate good intermediate images any more.

# image 00: POSCAR
0.6205393683339545 0.3748186251700154 0.6113134379103631 T T T
0.4407191996091184 0.3753464715751533 0.6109833865746312 T T T

#image 02: POSCAR
0.6205250119801456 0.8749946587628363 0.6126018270732655 T T T
0.4404841117364926 0.8751503266829158 0.6121692792622382 T T T

But by keying in nebmake.pl 00/POSCAR 02/POSCAR 1, i got 01POSCAR as
0.6205321901570500 0.1249066419664260 0.6119576324918160 T T T
0.4406016556728080 0.6252483991290350 0.6115763329184321 T T T

It seems that y values are not correct, but i cannot pinpoint where things went wrong. They are not so close to the edge of the box!
Help! I am using vtst-scripts947

I am attaching the files, and many thanks
Attachments
test.zip
(1.52 KiB) Downloaded 328 times
graeme
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Posts: 1999
Joined: Tue Apr 26, 2005 4:25 am
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Re: nebmake.pl bug?

Post by graeme »

The script is working as it should. The issue is that you are moving almost exactly 1/2 way across the box in the y-direction between images 0 and 2. In our script, we find the shortest path between the initial and final states relative to the periodic boundary conditions. For the first atom, it is slightly shorter to go along +y but for the second, it is closer along -y. If you just move the molecule a little closer between the 00 and 02 images, then it will interpolate as you expect it to.
kai
Posts: 55
Joined: Sun Oct 31, 2010 11:01 pm

Re: nebmake.pl bug?

Post by kai »

got it and thanks
rachita_panigrahi
Posts: 1
Joined: Sat Jan 23, 2021 3:53 am

Re: nebmake.pl bug?

Post by rachita_panigrahi »

while i m calculating NEB by using nebmake.pl script..so its showing (In vasp.pm::read_poscar, cannot open POSCAR00)...so can u help me...thanks in advance
Xingru Tan
Posts: 4
Joined: Thu Jul 01, 2021 7:00 am

Re: nebmake.pl bug?

Post by Xingru Tan »

I encountered the same problem. When I am trying to use the script nebmake. Error message appears(In vasp.pm::read_poscar, cannot open 'filename'). Can someone please help me?
Xingru Tan
Posts: 4
Joined: Thu Jul 01, 2021 7:00 am

Re: nebmake.pl bug?

Post by Xingru Tan »

rachita_panigrahi wrote:
> while i m calculating NEB by using nebmake.pl script..so its showing (In
> vasp.pm::read_poscar, cannot open POSCAR00)...so can u help me...thanks in
> advance

same error solved. Mine is due to typing the wrong dir of the two POSCAR file in the command. Double-check the command.
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