Atoms are in the same position. Unable to run.

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pranjal222
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Atoms are in the same position. Unable to run.

#1 Post by pranjal222 » Tue Nov 28, 2023 6:27 pm

Dear All,

Hope you are doing well.

I have the POSCAR file (coordinates below) in which Na and Bi are at the same position (this is what we expect as well in the experimental results and it is the same in the cif file too).

However when I run the program, I get the warning "The distance between some ions is very small. Please check the nearest neighbour list in the OUTCAR file. " Followed by this I get the error "Error EDDDAV: Call to ZHEGV failed. Returncode = 9 2 16".

I would like to know how can I proceed from here? Do I manually change some positions which will be closer to the real POSCAR file? If yes, what amount of deviation can be considered safe?

Kindly suggest.

Here is my POSCAR file.

Bi0.5 Na0.5 O3 Ti
1.0
5.5178999901 0.0000000000 0.0000000000
0.0000000000 5.5178999901 0.0000000000
0.0000000000 0.0000000000 3.9072999954
Na Bi Ti O
2 2 2 6
Direct
0.000000000 0.500000000 0.545000017
0.500000000 0.000000000 0.545000017
0.000000000 0.500000000 0.545000017
0.500000000 0.000000000 0.545000017
0.000000000 0.000000000 0.000000000
0.500000000 0.500000000 0.000000000
0.000000000 0.000000000 0.509999990
0.500000000 0.500000000 0.509999990
0.270999998 0.229000002 0.015000000
0.728999972 0.771000028 0.015000000
0.771000028 0.270999998 0.015000000
0.229000002 0.728999972 0.015000000


And Here is the INCAR file.
ISTART = 0
ICHARG = 2
INIWAV = 1
ENCUT = 500.00 eV
PREC = Accurate
LREAL = Auto
ISMEAR = 0
SIGMA = 0.01
EDIFF = 1.0E-8
NELM = 200
GGA = PE
NCORE = 04
NBANDS = 300
ADDGRID = .TRUE.

##Relaxation
NSW = 200
EDIFFG = -1.0E-4
IBRION = 1
POTIM = 0.5
ISIF = 7
ADDGRID = .TRUE.

LOPTICS =.TRUE.
CSHIFT = 0.1

Requesting your kind guidance.

I am very new to this type of simulations where the atoms take the similar positions.

Thank you.

Regards,
Pranjal

fabien_tran1
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Re: Atoms are in the same position. Unable to run.

#2 Post by fabien_tran1 » Tue Nov 28, 2023 9:06 pm

Hi,

Either the cif file is wrong or there is disorder in the system
https://chemistry.stackexchange.com/que ... he-lattice
and you would need to use a supercell for the simulation.

Besides, probably all programs for electronic-structure calculations can not handle such a situation and would crash.

pranjal222
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Re: Atoms are in the same position. Unable to run.

#3 Post by pranjal222 » Wed Nov 29, 2023 11:06 am

Dear Fabien,

Thanks for the reply and the link.

If I understood correctly. I should then create a supercell and make the ratio of Sodium and Bismuth 50:50 but at different location? I mean remove some Na and keep only Bi and in other place remove Bi and keep Na.

This is because there is a 50% probability that at that location, it can either be a Bi or a Na atom.

Could you please comment if my thinking is correct.

Thank you, once again.

Regards,
Pranjal

fabien_tran1
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Re: Atoms are in the same position. Unable to run.

#4 Post by fabien_tran1 » Wed Nov 29, 2023 11:21 am

I don't really know since I have never studied this system. The most important is first to read the paper(s) about this system to figure out what is its structure.

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