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Posted: **Thu Feb 08, 2024 7:52 pm**

Hello,
I have a problem with calculations in VASP.

|     The distance between some ions is very small. Please check the          |
|     nearest-neighbor list in the OUTCAR file.                               |
|     I HOPE YOU KNOW WHAT YOU ARE DOING!

How can i resolve this problem?
Optimizing geometry

InCAR

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general:
 System = VASP-OPT
 ISMEAR = 0
 SIGMA = 0.1
 ENMAX  =  400
 IBRION=2
 ISIF=3
 NSW=4000
 EDIFF  = 0.1E-05
 EDIFFG = -0.001
 LPLANE=.TRUE.
 #NCORE=6
 #NPAR=2
 LSCALU=.False.
 NSIM = 4

K-point

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K-Points
 0
Monkhorst Pack
 8 8 8
0  0  0

Poscar

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622375-NH3BH3
1.0
        5.5409998894         0.0000000000         0.0000000000
        0.0000000000         4.7049999237         0.0000000000
        0.0000000000         0.0000000000         5.0237002373
    N    B    H
    3    3   18
Cartesian
0.000000    1.156960    1.567897
5.541000    1.156960    1.567897
2.770500    3.548041    4.079747
0.000000    0.795145    0.010047
5.541000    0.795145    0.010047
2.770500    3.909855    2.521897
0.000000    1.947870    1.672892
0.781281    0.785735    1.984362
0.000000   -0.329350   -0.030142
0.858855    1.293875   -0.411943
0.781281    0.785735    1.984362
0.858855    1.293875   -0.411943
5.541000    1.947870    1.672892
6.322281    0.785735    1.984362
5.541000   -0.329350   -0.030142
6.399855    1.293875   -0.411943
4.759719    0.785735    1.984362
4.682145    1.293875   -0.411943
2.770500    2.757130    4.184742
1.989219    3.919265    4.496212
2.770500    5.034350    2.481708
1.911645    3.411125    2.099907
3.551781    3.919265    4.496212
3.629355    3.411125    2.099907

Posted: **Fri Feb 09, 2024 8:18 am**

Hi,

Your POSCAR file contains overlapping atoms. The first two atom positions

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0.000000    1.156960    1.567897
5.541000    1.156960    1.567897

are the same under the periodic boundary conditions of the simulation cell. You can see this by adding the first lattice vector

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5.5409998894         0.0000000000         0.0000000000

to the first atom position, which yields the second atom position.

Please, make sure that your POSCAR does not contain such duplicate coordinates. That will fix your problem.

Posted: **Fri Feb 09, 2024 10:06 am**

How can fix for ammonia borane system?
I need model for whole unitt cell or one molecule?

Posted: **Fri Feb 09, 2024 12:21 pm**

I converted the cif file you provided into a POSCAR file. Here is the result:

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POSCAR from cif
1.0
     5.5410000000       0.0000000000       0.0000000000
     0.0000000000       4.7050000000       0.0000000000
     0.0000000000       0.0000000000       5.0237000000
N B H
2 2 12
Direct
     0.000000000     0.245900000     0.312100000
     0.500000000     0.754100000     0.812100000
     0.000000000     0.169000000     0.002000000
     0.500000000     0.831000000     0.502000000
     0.000000000     0.414000000     0.333000000
     0.500000000     0.586000000     0.833000000
     0.141000000     0.167000000     0.395000000
     0.359000000     0.833000000     0.895000000
     0.859000000     0.167000000     0.395000000
     0.641000000     0.833000000     0.895000000
     0.000000000     0.930000000     0.994000000
     0.500000000     0.070000000     0.494000000
     0.155000000     0.275000000     0.918000000
     0.345000000     0.725000000     0.418000000
     0.845000000     0.275000000     0.918000000
     0.655000000     0.725000000     0.418000000

This runs without any issues. Notice how the number of atoms is different from the POSCAR you showed in your first post. When constructing POSCAR files by hand, please, make sure that you first read the online documentation on the POSCAR file format.

I hope that this helps resolve the issue.

My Community

The distance between some ions is very small.

The distance between some ions is very small.

Re: The distance between some ions is very small.

Re: The distance between some ions is very small.

Re: The distance between some ions is very small.