Warning :The distance between some ions is very small

[sabmaj]

Dear all,

I wanted to simulate the equilibrium structure of a trilayer graphite.
I got the following warning message and calculation never started:

WARNING : The distance between some ions is very small please check the nearest neigbor list in the OUTCAR file
I HOPE YOU KNOW, WHAT YOU ARE DOING.

I think that the main problem in my definition of the supercell:
It is a honeycomb structure with hexagonal symmetry. This is the inforamtion I have :
Symmetry: Hexagonal a=b;c; alpha=beta=90; gamma=120
P63/mmc

Graphite:

a=b=2.45600000; c=6.69600000
d=c/2=3.34800000
c/a=2.72638436

Primitive vectors
a(1) = 1.22800000 -2.12695839 0.00000000
a(2) = 1.22800000 2.12695839 0.00000000
a(3) = 0.00000000 0.00000000 6.69600000


Volume = 34.97863049


Basis Vectors: vmn
Atom Lattice Coordinates Cartesian Coordinates

C 0.00000000 0.00000000 0.25000000 0.00000000 0.00000000 1.67400000
C 0.00000000 0.00000000 0.75000000 0.00000000 0.00000000 5.02200000
C 0.33333333 0.66666667 0.25000000 1.22800000 0.70898613 1.67400000
C 0.66666667 0.33333333 0.75000000 1.22800000 -0.70898613 5.02200000
------------------------------------------------------------------
I used the following POSCAR:
C
1.00000000000000
7.36800000000000 0.00000000000000 0.00000000000000
0.00000000000000 7.09000000000000 0.00000000000000
0.00000000000000 0.00000000000000 26.69600000000000
75
Direct
0.00000000000000 0.00000000000000 0.74917590650285
0.00000000000000 0.00000000000000 0.00000000000000
0.00000000000000 0.40000000000000 0.74917590650285
0.00000000000000 0.60000000000000 0.87458795325142
0.00000000000000 0.40000000000000 0.00000000000000
0.00000000000000 0.80000000000000 0.74917590650285
0.16666666666667 0.70000000000000 0.74917590650285
0.00000000000000 0.80000000000000 0.87458795325142
0.00000000000000 0.80000000000000 0.00000000000000
0.16666666666667 0.90000000000000 0.87458795325142
0.16666666666667 0.70000000000000 0.00000000000000
0.33333333333333 0.00000000000000 0.74917590650285
0.33333333333333 0.00000000000000 0.00000000000000
0.00000000000000 0.00000000000000 0.87458795325142
0.00000000000000 0.20000000000000 0.74917590650285
0.16666666666667 0.10000000000000 0.74917590650285
0.00000000000000 0.20000000000000 0.87458795325142
0.00000000000000 0.20000000000000 0.00000000000000
0.16666666666667 0.30000000000000 0.87458795325142
0.16666666666667 0.10000000000000 0.00000000000000
0.16666666666667 0.50000000000000 0.74917590650285
0.33333333333333 0.40000000000000 0.74917590650285
0.16666666666667 0.50000000000000 0.87458795325142
0.16666666666667 0.50000000000000 0.00000000000000
0.33333333333333 0.60000000000000 0.87458795325142
0.33333333333333 0.40000000000000 0.00000000000000
0.33333333333333 0.80000000000000 0.74917590650285
0.50000000000000 0.70000000000000 0.74917590650285
0.33333333333333 0.80000000000000 0.87458795325142
0.33333333333333 0.80000000000000 0.00000000000000
0.50000000000000 0.90000000000000 0.87458795325142
0.50000000000000 0.70000000000000 0.00000000000000
0.66666666666667 0.00000000000000 0.74917590650285
0.66666666666667 0.00000000000000 0.00000000000000
0.33333333333333 0.00000000000000 0.87458795325142
0.33333333333333 0.20000000000000 0.74917590650285
0.50000000000000 0.10000000000000 0.74917590650285
0.33333333333333 0.20000000000000 0.87458795325142
0.33333333333333 0.20000000000000 0.00000000000000
0.50000000000000 0.30000000000000 0.87458795325142
0.50000000000000 0.10000000000000 0.00000000000000
0.50000000000000 0.50000000000000 0.74917590650285
0.66666666666667 0.40000000000000 0.74917590650285
0.50000000000000 0.50000000000000 0.87458795325142
0.50000000000000 0.50000000000000 0.00000000000000
0.66666666666667 0.60000000000000 0.87458795325142
0.66666666666667 0.40000000000000 0.00000000000000
0.66666666666667 0.80000000000000 0.74917590650285
0.83333333333333 0.70000000000000 0.74917590650285
0.66666666666667 0.80000000000000 0.87458795325142
0.66666666666667 0.80000000000000 0.00000000000000
0.83333333333333 0.90000000000000 0.87458795325142
0.83333333333333 0.70000000000000 0.00000000000000
0.00000000000000 0.00000000000000 0.74917590650285
0.00000000000000 0.00000000000000 0.00000000000000
0.66666666666667 0.00000000000000 0.87458795325142
0.66666666666667 0.20000000000000 0.74917590650285
0.83333333333333 0.10000000000000 0.74917590650285
0.66666666666667 0.20000000000000 0.87458795325142
0.66666666666667 0.20000000000000 0.00000000000000
0.83333333333333 0.30000000000000 0.87458795325142
0.83333333333333 0.10000000000000 0.00000000000000
0.83333333333333 0.50000000000000 0.74917590650285
0.00000000000000 0.40000000000000 0.74917590650285
0.83333333333333 0.50000000000000 0.87458795325142
0.83333333333333 0.50000000000000 0.00000000000000
0.00000000000000 0.60000000000000 0.87458795325142
0.00000000000000 0.40000000000000 0.00000000000000
0.00000000000000 0.80000000000000 0.74917590650285
0.00000000000000 0.80000000000000 0.87458795325142
0.00000000000000 0.80000000000000 0.00000000000000
0.00000000000000 0.00000000000000 0.87458795325142
0.00000000000000 0.20000000000000 0.74917590650285
0.00000000000000 0.20000000000000 0.87458795325142
0.00000000000000 0.20000000000000 0.00000000000000

Is there any thing wrong with the POSCAR and supercell definition: I wanted the graphite to be in a vacuum region in the z direction of 20Angstrom.
Please could you help?
I appreciate it.

Thanks in advance!

[mrm]

Hello Sabmaj,

I did not look at you POSCAR in detail but I can suggest a couple of things to be careful about:

1) Make sure that while you are choosing your Cartesian coordinates you should keep in mind that they will all be multiplied by the "lattice constant" at the top of the POSCAR (which appears to be "one" in your case". However, the lattice vectors will also be multiplied by this constant.

2) I have found that VMD viewer (found on UIUC.edu website for free) is really great for looking at POSCAR files. It can view them directly without converting to some other format (e.g. PDB) and it can also understand Direct or Cartesian formats of POSCAR. You can view your POSCAR, measure the bond lengths, and even repeat periodically to make sure your supercell is defined correctly.

I hope this helps! Enjoy.

[sabmaj]

Thank you mrm for your response.
I tried to visualize the structure with other molecular viewer and it looks fine for me.
I believe that the problem is in the supercell.
Is there any way to check if the supercell is defined correctly? Does any one have a suggestion?

Thank you again.